Index
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes All Packages
All Classes All Packages
All Classes All Packages
A
- absolute() - Method in class org.anchoranalysis.spatial.point.Tuple3d
- AbsoluteValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
- AbsoluteValue() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AbsoluteValue
- accept(int) - Method in interface org.anchoranalysis.core.functional.checked.CheckedIntConsumer
- accept(int, int) - Method in interface org.anchoranalysis.math.histogram.Histogram.BinConsumer
- accept(int, int) - Method in interface org.anchoranalysis.spatial.point.consumer.ScalarTwoDimensionalConsumer
-
Accepts a point like with a
Consumerin general. - accept(int, int, int) - Method in interface org.anchoranalysis.spatial.point.consumer.OffsettedScalarTwoDimensionalConsumer
-
Accepts a point
- accept(int, int, int) - Method in interface org.anchoranalysis.spatial.point.consumer.ScalarThreeDimensionalConsumer
-
Accepts a point like with a
Consumerin general. - accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
- accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
- accept(ObjectMask) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.UpdatableBeforeCondition
- accept(ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
- accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.BeforeCondition
- accept(ObjectMask, ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.DistanceCondition
- accept(ObjectMask, ObjectMask, ObjectMask) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.AfterCondition
- accept(ObjectMask, ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
- accept(ParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.check.AtLeastZSlices
- accept(ParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.check.CheckParsedFilePathBag
- accept(Point2i) - Method in interface org.anchoranalysis.spatial.point.consumer.PointTwoDimensionalConsumer
-
Accepts a point like with a
Consumerin general. - accept(Point2i, int) - Method in interface org.anchoranalysis.spatial.point.consumer.OffsettedPointTwoDimensionalConsumer
-
Accepts a point like with a
Consumerin general. - accept(S) - Method in interface org.anchoranalysis.core.functional.checked.CheckedConsumer
- accept(S, T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedBiConsumer
-
Calls the function
- accepted() - Method in interface org.anchoranalysis.annotation.mark.DualMarks
-
The accepted marks.
- acceptIteration(Voxels<UnsignedByteBuffer>, BinaryValues) - Method in interface org.anchoranalysis.image.voxel.object.morphological.accept.AcceptIterationConditon
- acceptIteration(Voxels<UnsignedByteBuffer>, BinaryValues) - Method in class org.anchoranalysis.image.voxel.object.morphological.accept.AcceptIterationList
- acceptIteration(Voxels<UnsignedByteBuffer>, BinaryValues) - Method in class org.anchoranalysis.image.voxel.object.morphological.accept.RejectIterationIfAllHigh
- acceptIteration(Voxels<UnsignedByteBuffer>, BinaryValues) - Method in class org.anchoranalysis.image.voxel.object.morphological.accept.RejectIterationIfLowDisconnected
- AcceptIterationConditon - Interface in org.anchoranalysis.image.voxel.object.morphological.accept
-
A condition that must be fulfilled for a particular iteration of a morphological operation to be accepted.
- AcceptIterationList - Class in org.anchoranalysis.image.voxel.object.morphological.accept
- AcceptIterationList() - Constructor for class org.anchoranalysis.image.voxel.object.morphological.accept.AcceptIterationList
- acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
- acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.BinaryKernel
- acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
- acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.density.DensityKernel
- acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.density.MaxDensityKernel3
-
This method is deliberately not broken into smaller pieces to avoid inlining.
- acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3
-
This method is deliberately not broken into smaller pieces to avoid inlining.
- acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3ZOnly
- acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.ErosionKernel3
-
This method is deliberately not broken into smaller pieces to avoid inlining.
- acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3
-
This method is deliberately not broken into smaller pieces to avoid inlining.
- acceptPoint(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3NeighborMatchValue
-
This method is deliberately not broken into smaller pieces to avoid inlining.
- acceptProposal(ToDoubleFunction<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- accepts(Class<?>) - Method in interface org.anchoranalysis.bean.initializable.property.PropertyDefiner
- accepts(Class<?>) - Method in class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
- acceptsAsSource(Class<?>) - Method in class org.anchoranalysis.bean.initializable.property.ExtractFromParam
-
Are the source-parameters acceptable for extraction? *
- AccessObjectMask<T> - Interface in org.anchoranalysis.image.core.object.scale
-
Provides functions to provide access and creation to/from the object-mask representation of a generic type.
- AccptProbCalculator<T> - Class in org.anchoranalysis.plugin.mpp.segment.optimization
- AccptProbCalculator(AnnealScheme, ExtractScoreSize<T>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.AccptProbCalculator
- activateDebugMode(String) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
-
Activates debug-mode
- add(double) - Method in class org.anchoranalysis.feature.energy.EnergyTotal
- add(double) - Method in class org.anchoranalysis.plot.AxisLimits
- add(double) - Method in class org.anchoranalysis.plugin.annotation.comparison.RangeSum
- add(double, double, double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- add(int, int, int) - Method in class org.anchoranalysis.spatial.box.PointRange
- add(int, long) - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
- add(int, String) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
- add(int, RGBColor) - Method in class org.anchoranalysis.core.color.ColorList
- add(int, UpdatableMarkSet) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- add(Color) - Method in class org.anchoranalysis.core.color.ColorList
- add(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.task.InputTypesExpected
- add(Double) - Method in class org.anchoranalysis.mpp.probmap.ProbWeights
- add(Exception) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
- add(Exception) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- add(Exception) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
- add(String) - Method in interface org.anchoranalysis.bean.StringBeanCollection
- add(String) - Method in class org.anchoranalysis.bean.StringList
- add(String) - Method in class org.anchoranalysis.bean.StringSet
- add(String) - Method in class org.anchoranalysis.feature.name.FeatureNameList
-
Adds a feature-name
- add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
- add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- add(String) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
- add(String, boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
-
Adds a new output-name to the set of recorded names.
- add(String, int) - Method in class org.anchoranalysis.feature.name.FeatureNameMapToIndex
-
Adds a new featureName and index
- add(String, int) - Method in class org.anchoranalysis.overlay.OverlayProperties
- add(String, String) - Method in class org.anchoranalysis.overlay.OverlayProperties
- add(String, StoreSupplier<Stack>) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
- add(String, StoreSupplier<TimeSequence>) - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
- add(String, StoreSupplier<TimeSequence>) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
- add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
- add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
- add(String, StoreSupplier<T>) - Method in interface org.anchoranalysis.core.identifier.provider.store.NamedProviderStore
- add(String, StoreSupplier<T>) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap
-
Adds an entry to the map
- add(String, StoreSupplier<T>) - Method in class org.anchoranalysis.mpp.io.input.OperationMap
- add(String, Feature<T>) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
-
Adds a named-feature to the store.
- add(String, Stack) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
- add(String, Stack) - Method in class org.anchoranalysis.image.core.stack.NamedStacksUniformSize
- add(String, Generator<T>) - Method in class org.anchoranalysis.io.generator.combined.CombinedListGenerator
- add(String, EnergyScheme) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
- add(String, Mark) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
- add(String, Mark) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- add(String, Mark) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
- add(String, S, NamedProviderStore<D>, CheckedFunction<S, D, OperationFailedException>) - Static method in class org.anchoranalysis.bean.store.BeanStoreAdder
-
Adds an item a container (using a bridge) and explicitly specifying a new name
- add(String, T) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
- add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
- add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
- add(Path) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
- add(Optional<String>, String, S) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName
-
Adds an item with an identifier
- add(NamedBean<?>) - Method in class org.anchoranalysis.bean.define.Define
-
Adds a named-bean to our definitions, using the {#link GroupingRoot} annotation to determine a group where definitions are stored.
- add(PermutationSetter) - Method in class org.anchoranalysis.bean.permute.setter.PermutationSetterList
- add(RGBColor) - Method in class org.anchoranalysis.core.color.ColorList
- add(NameValue<T>) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
- add(NamedProvider<T>) - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
- add(NameValueSet<T>) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
- add(StatefulMessageLogger) - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
- add(SubmittedJob) - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- add(Feature<? extends T>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- add(EnergyTotal) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- add(ResultsVector) - Method in class org.anchoranalysis.feature.results.ResultsVectorList
- add(CacheTransferSource<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
- add(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
- add(Seed) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- add(Stack) - Method in class org.anchoranalysis.image.core.stack.TimeSequence
- add(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
- add(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannelsSimple
- add(AcceptIterationConditon) - Method in class org.anchoranalysis.image.voxel.object.morphological.accept.AcceptIterationList
- add(ObjectMask) - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
- add(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- add(VoxelStatistics) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
- add(VoxelsWrapper) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
- add(MutableDirectory) - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
- add(FileType[]) - Method in class org.anchoranalysis.io.generator.ConcatenateFileTypes
- add(OutputtedFile) - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
- add(OutputtedFile) - Method in class org.anchoranalysis.io.manifest.directory.Subdirectory
- add(EnergySavedInd, VoxelizedMarkMemo, EnergyStackWithoutParams, EnergySchemeWithSharedFeatures) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
- add(MemoCollection, VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- add(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- add(Mark, Color) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- add(Mark, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- add(UpdatableMarkSet) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- add(MemoForIndex) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
- add(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- add(MemoForIndex, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.set.UpdatableMarkSet
- add(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
- add(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
- add(VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- add(CreateProposalVisualization) - Method in class org.anchoranalysis.mpp.proposer.visualization.CreateProposeVisualizationList
- add(TerminationCondition) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
- add(WeightedKernel<T>) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
- add(AggregateReceiver<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
- add(FeedbackReceiver<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
- add(PeriodReceiver<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverList
- add(IndexByRegion<T>) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
- add(Overlay) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- add(Overlay, RGBColor) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- add(AnnotationGroup<T>) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
- add(LevelResult) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
- add(FileDetails) - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
- add(BoundingBox) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
- add(BoundingBox, T) - Method in class org.anchoranalysis.spatial.rtree.RTree
-
Adds a bounding-box with a corresponding index.
- add(Point2d) - Method in class org.anchoranalysis.spatial.point.Point2d
- add(Point2i) - Method in class org.anchoranalysis.spatial.point.Point2d
- add(Point2i) - Method in class org.anchoranalysis.spatial.point.Point2i
- add(Point3i) - Method in class org.anchoranalysis.spatial.box.PointRange
- add(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- add(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- add(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- add(S, T) - Method in interface org.anchoranalysis.plugin.image.task.grouped.AddToAggregateItem
- add(T) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing
-
Outputs an additional element in the sequence.
- add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
- add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer
-
Adds a element to the summary.
- add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
- add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
- add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
- add(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
- add(T, String) - Method in class org.anchoranalysis.image.experiment.label.FileLabelMap
- add(T, S) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed
-
Outputs an additional element in the sequence.
- addAcceptedAnnotation(AssignmentOverlapFromPairs) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
- addAcceptedAnnotation(T) - Method in interface org.anchoranalysis.plugin.annotation.comparison.AddAnnotation
- addAcceptedAnnotation(T) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- addAcceptedAnnotation(T) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
- addAdditionalOptions(Options) - Method in class org.anchoranalysis.launcher.config.LauncherConfig
- addAdditionalOptions(Options) - Static method in class org.anchoranalysis.launcher.options.CommandLineOptions
- addAll(int, Collection<? extends UpdatableMarkSet>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- addAll(Collection<? extends ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- addAll(Collection<? extends UpdatableMarkSet>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- addAll(Collection<AnnotationGroup<T>>) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
- addAll(Define) - Method in class org.anchoranalysis.bean.define.Define
-
Adds all the named-beans (shallow copy) from source to th ecurrent map
- addAll(ColorList) - Method in class org.anchoranalysis.core.color.ColorList
- addAll(FeatureList<? extends T>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- addAll(ObjectCollection) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- addAll(ColoredMarks) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- addAll(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- addAll(MarkCollection, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- addAll(MemoForIndex) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
- addAll(OverlayCollection) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- addAllOutputNamesTo(OutputEnabledMutable) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
-
Adds all possible output-names to a
OutputEnabledMutable. - addAllScaled(ColorList, double) - Method in class org.anchoranalysis.core.color.ColorList
- addAllToUpdatablePairList(ListUpdatableMarkSetCollection) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- AddAnnotation<T extends Assignment> - Interface in org.anchoranalysis.plugin.annotation.comparison
- addBasicOptions(Options) - Static method in class org.anchoranalysis.launcher.options.CommandLineOptions
- addBean(String, Object) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
- addBean(String, Object) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- addBean(String, Object) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
- addBeansFromList(Define, List<NamedBean<?>>) - Static method in class org.anchoranalysis.bean.define.adder.DefineAdderUtilities
- addBlankChannel() - Method in class org.anchoranalysis.image.core.stack.Stack
- addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
- addBoundChangeListener(BoundChangeListener) - Method in interface org.anchoranalysis.core.index.bounded.BoundedRangeIncompleteDynamic
- addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
- addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
- addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
- addBoundChangeListener(BoundChangeListener) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
- addBuffer(FloatBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferFloat
- addBuffer(UnsignedByteBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferByte
- addBuffer(UnsignedIntBuffer, UnsignedIntBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferInt
- addBuffer(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferShort
- addBuffer(T, T) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBuffer
- addChangeID(Mark, Color) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- addChangeID(Mark, RGBColor) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- addChannel(Channel) - Method in class org.anchoranalysis.image.core.stack.Stack
- addChannel(Channel) - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
- addChannelsFrom(Stack) - Method in class org.anchoranalysis.image.core.stack.Stack
- AddConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
- AddConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.AddConstant
- AddConstantTo<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
- AddConstantTo() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AddConstantTo
- AddCriteria<T> - Interface in org.anchoranalysis.mpp.feature.addcriteria
-
Add Criteria
- AddCriteriaDistanceTo - Class in org.anchoranalysis.plugin.mpp.bean.addcriteria
- AddCriteriaDistanceTo() - Constructor for class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
- AddCriteriaEnergyPair - Class in org.anchoranalysis.mpp.feature.addcriteria
- AddCriteriaEnergyPair(FeatureList<FeatureInputPairMemo>, AddCriteriaPair) - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
- AddCriteriaFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.addcriteria
- AddCriteriaFeatureRelationThreshold() - Constructor for class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
- AddCriteriaNever<T> - Class in org.anchoranalysis.mpp.feature.addcriteria
- AddCriteriaNever() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
- AddCriteriaOr - Class in org.anchoranalysis.mpp.feature.addcriteria
- AddCriteriaOr() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
- AddCriteriaPair - Class in org.anchoranalysis.mpp.feature.addcriteria
- AddCriteriaPair() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
- addCustomNames(FeatureList<?>) - Method in class org.anchoranalysis.feature.name.FeatureNameList
-
Add the customNames of a feature
- addCustomNamesWithPrefix(String, FeatureList<?>) - Method in class org.anchoranalysis.feature.name.FeatureNameList
-
Add the customNames of a feature with a Prefix
- AddDistanceTransform - Class in org.anchoranalysis.plugin.fiji.bean.define
-
Performs a Watershed on an EDT transform by bundling together several other beans
- AddDistanceTransform() - Constructor for class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
- addDoubleAsString(String, double) - Method in class org.anchoranalysis.overlay.OverlayProperties
- AddDualTransformer - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
- AddDualTransformer() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.AddDualTransformer
- addEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
-
Add an edge between two vertices.
- addEdge(V, V, P) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
Add an edge between two vertices.
- AddEdgeFilters - Class in org.anchoranalysis.plugin.imagej.bean.define
- AddEdgeFilters() - Constructor for class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
- addEdges(V, Collection<V>) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
-
Adds edge(s) from the vertex
fromto each element intoCollection. - addEnabledOutputFirst(String...) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
-
Adds enabled first-level outputs.
- addEnabledOutputs(OutputEnabledMutable) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
-
Adds enabled outputs from another
OutputEnabledMutable. - addEnabledOutputSecond(String, String...) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
-
Adds enabled second-level outputs.
- AddEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
- AddEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.AddEnergy
- addErrorDescription(StringBuilder) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
- addErrorDescription(StringBuilder) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- addErrorDescription(StringBuilder) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
- addErrorLevel(String) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
- addErrorLevel(String, AnchorBean<?>) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
- addFeatureListToStore(FeatureList<T>, String, boolean, NamedFeatureStore<T>) - Static method in class org.anchoranalysis.feature.list.FeatureListStoreUtilities
-
Adds a feature-list to the store
- addFeatureListToStoreNoDuplicateDirectly(NamedProvider<FeatureList<FeatureInput>>, SharedFeatureMulti) - Static method in class org.anchoranalysis.feature.list.FeatureListStoreUtilities
- addField(Field) - Method in class org.anchoranalysis.bean.permute.setter.PermutationSetterSingle
- addFormatted(String, Object...) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
- addFormatted(String, Object...) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- addFormatted(String, Object...) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
- addForSlice(int, int) - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
- addForSlice(int, int) - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
- addFrom(List<NamedBean<?>>) - Method in class org.anchoranalysis.bean.BeanInstanceMap
-
Populates from a list of
NamedBean. - addFrom(BeanInstanceMap) - Method in class org.anchoranalysis.bean.BeanInstanceMap
-
Populates the entries from another BeanInstanceMap
- addFrom(NamedProvider<Stack>) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
- addFromWithPrefix(NamedProvider<Stack>, String) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
- addFromXmlFile(Path) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap
-
Adds root-paths contained in a list of XML Beans in an xml file
- addHistogram(Histogram) - Method in class org.anchoranalysis.math.histogram.Histogram
- addIgnoreInfinity(double) - Method in class org.anchoranalysis.plot.AxisLimits
- addIter(int) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNode
- addIter(int) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- addIter(int) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
- addLabelToDataset(DefaultCategoryDataset, T, int, String, String) - Method in class org.anchoranalysis.plot.index.BarPlot
- addLabelToDataset(DefaultBoxAndWhiskerCategoryDataset, T, int, String, String) - Method in class org.anchoranalysis.plot.index.BoxPlot
- addLabelToDataset(S, T, int, String, String) - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
- addLeftObject(ObjectMask) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- addLeftObjects(ObjectCollection) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- addListOfBeansToCollection(String, HierarchicalConfiguration, Collection<T>, Object) - Static method in class org.anchoranalysis.bean.xml.factory.HelperListUtilities
- addManifestExperimentFileSet(Collection<File>, ManifestDeserializer, Logger) - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
- addMultiple(RGBColor, int) - Method in class org.anchoranalysis.core.color.ColorList
- addNewPath(Point3i, Point3i) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
-
Adds a new path with a point
- addNoDuplicate(FeatureList<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
- addObjectsNoBoundingBoxChange(Collection<T>) - Method in class org.anchoranalysis.spatial.box.BoundedList
-
Adds elements without changing the bounding-box
- addObjectsToGraph(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
- addObjectsWithColor(ObjectCollectionProvider, RGBColor) - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection
-
Adds objects from a
ObjectCollectionProviderall with one specific color - addOperationRecorder(WriteOperationRecorder) - Method in class org.anchoranalysis.io.output.outputter.Outputter
- addOperationRecorder(WriteOperationRecorder) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
-
Adds an additional operation recorder alongside any existing recorders.
- addPair(ObjectMask, ObjectMask, double) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- addPointsInMark(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- addPreserveName(List<NamedBean<S>>, NamedProviderStore<D>, CheckedFunction<S, D, OperationFailedException>) - Static method in class org.anchoranalysis.bean.store.BeanStoreAdder
-
Adds a list of named-items a container (using a bridge) using the same names in the destination container
- addPreserveNameEmbedded(List<NamedBean<S>>, NamedProviderStore<D>, CheckedFunction<NamedBean<S>, D, OperationFailedException>) - Static method in class org.anchoranalysis.bean.store.BeanStoreAdder
-
Adds a list of named-items to a container (using a bridge) using the same names in the destination container
- addProperties(NameValueSet<String>) - Method in class org.anchoranalysis.image.core.orientation.Orientation
- addProperties(NameValueSet<String>) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- addProperties(NameValueSet<String>) - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
- addProperties(NameValueSet<String>) - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
- addPropertiesToMask(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.orientation.Orientation
- addPropertiesToMask(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- addPropertiesToMask(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
- addPropertiesToMask(ObjectWithProperties) - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
- addResultsFor(RowLabels, ResultsVector) - Method in class org.anchoranalysis.feature.io.results.group.GroupWriter
-
Adds a result to the group-writer, but doesn't write yet.
- addResultsFor(RowLabels, ResultsVector) - Method in class org.anchoranalysis.feature.io.results.ResultsWriter
-
Adds feature-calculation results to be written.
- addResultsFor(RowLabels, ResultsVectorWithThumbnail) - Method in interface org.anchoranalysis.plugin.image.task.feature.ExportFeatureResultsAdder
-
Adds labeled results (which makes a row in a feature-table, and possibly other outputs).
- addResultsFor(RowLabels, ResultsVectorWithThumbnail) - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
- addRightObject(ObjectMask) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- addRightObjects(ObjectCollection) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- addRow(List<TypedValue>) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter
-
Directly adds a row in the form of typed-values.
- addRow(RowLabels, ResultsVector) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter
-
Directly adds a row of feature-values.
- addShift(ReadableTuple3i) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
-
Adds a shift to each point (modifying the existing points in memory), and returns them as a list
- addSkippedAnnotationImage() - Method in interface org.anchoranalysis.plugin.annotation.comparison.AddAnnotation
- addSkippedAnnotationImage() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- addSkippedAnnotationImage() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
- addTo(Define) - Method in class org.anchoranalysis.bean.define.adder.Concatenate
- addTo(Define) - Method in interface org.anchoranalysis.bean.define.adder.DefineAdder
- addTo(Define) - Method in class org.anchoranalysis.bean.define.adder.FromXmlList
- addTo(Define) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
- addTo(Define) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
- addTo(Define) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
- addTo(ObjectMask, int) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic
-
Adds a constant-value to each voxel but only for voxels inside an object-mask
- addTo(S, T) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName
- AddToAggregateItem<S,T> - Interface in org.anchoranalysis.plugin.image.task.grouped
-
Adds an individual-item to an aggregate-item
- AddToDefaults - Class in org.anchoranalysis.io.output.bean.rules
-
Adds additional outputs-names to be enabled to the defaults.
- AddToDefaults() - Constructor for class org.anchoranalysis.io.output.bean.rules.AddToDefaults
- addToErrorNode(ErrorNode) - Method in exception org.anchoranalysis.mpp.proposer.error.ErrorNodeException
- addToKeyValueParamsCollection(String, KeyValueParams) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- addToManager(MultiInputManager, String, String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManager
- addToMarks(ColoredMarks) - Method in interface org.anchoranalysis.mpp.proposer.visualization.CreateProposalVisualization
- addToMarks(ColoredMarks) - Method in class org.anchoranalysis.mpp.proposer.visualization.CreateProposeVisualizationList
- addToRow(List<TypedValue>) - Method in class org.anchoranalysis.feature.io.csv.RowLabels
-
Adds the identifiers to a row to be outputted in a features CSV.
- addToSharedObjects(MPPInitParams, ImageInitParams) - Method in interface org.anchoranalysis.mpp.io.input.InputForMPPBean
- addToSharedObjects(MPPInitParams, ImageInitParams) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- addToSharedObjects(MPPInitParams, ImageInitParams) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
- addToStackCollection(String, StackProvider) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- addToStackCollection(String, Stack) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- addToStore(NamedProviderStore<TimeSequence>) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
- addToStore(NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
- addToStore(NamedProviderStore<T>) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap
-
Copies all the existing entries into a NamedProvierStore
- addToStore(NamedProviderStore<T>) - Method in class org.anchoranalysis.mpp.io.input.OperationMap
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- addToStoreInferNames(NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- addToStoreWithName(String, NamedProviderStore<TimeSequence>, int, ProgressReporter) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
- addToTypeValueCollection(Collection<TypedValue>, int) - Method in class org.anchoranalysis.feature.results.ResultsVector
- addToUpdatablePairList(ListUpdatableMarkSetCollection, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- addToVoxelList(int, int, int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
- addUnannotatedImage() - Method in interface org.anchoranalysis.plugin.annotation.comparison.AddAnnotation
- addUnannotatedImage() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- addUnannotatedImage() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
- addUncoupledJobs(Collection<File>, ManifestDeserializer, Logger) - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
-
Adds job-manifests that don't have corresponding experiment-manifests.
- addUnused(Histogram) - Method in class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactoryHistogramReuse
- addUnused(Histogram) - Method in class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitonFactoryHistogram
- addUnused(T) - Method in interface org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactory
- addVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
-
Adds a vertex.
- addVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
Adds a vertex.
- addVisitedPoint(Point3i) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
-
Adds a visited-point to an existing path, or else makes a new one
- addWeightedKernelFactories(List<WeightedKernel<T>>) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposerOption
- addWeightedKernelFactories(List<WeightedKernel<T>>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
- addWeightedKernelFactories(List<WeightedKernel<T>>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
- addWithIndex(RGBColor) - Method in class org.anchoranalysis.core.color.ColorList
- addWithName(Define, String, AnchorBean<?>) - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
- addWithUnits(String, double, DoubleUnaryOperator, SpatialUnits.UnitSuffix) - Method in class org.anchoranalysis.overlay.OverlayProperties
- AdjacentFile - Class in org.anchoranalysis.plugin.quick.bean.input
- AdjacentFile() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile
- adjacentVerticesOutgoing(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
-
The vertices that are connected to a particular vertex by an outgoing edge
- adjacentVerticesOutgoing(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
The vertices that are connected to a particular vertex by an outgoing edge
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.experiment.bean.task.TaskWithoutSharedState
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- afterAllJobsAreExecuted(NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- afterAllJobsAreExecuted(OutputSequenceIncrementing<Stack>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- afterAllJobsAreExecuted(CSVWriter, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
- afterAllJobsAreExecuted(ExperimentState, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
- afterAllJobsAreExecuted(AggregateSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
- afterAllJobsAreExecuted(SharedState<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- afterAllJobsAreExecuted(SharedStateExportFeatures<S>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
- afterAllJobsAreExecuted(GroupedSharedState<S, T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
- afterAllJobsAreExecuted(SharedStateFilteredImageOutput<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
- afterAllJobsAreExecuted(SharedStateSegmentInstance<T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
- afterAllJobsAreExecuted(SharedStateSelectedSlice, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
- afterAllJobsAreExecuted(Summarizer<S>, InputOutputContext) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
- afterAllJobsAreExecuted(FromCSVSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
- afterAllJobsAreExecuted(S, InputOutputContext) - Method in class org.anchoranalysis.experiment.bean.task.Task
-
Called once after all calls to
Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>). - afterAllJobsAreExecuted(S, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
- AfterCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
- afterCopying(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
- afterCopying(Path, boolean) - Method in interface org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNaming
- afterCopying(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
- afterCopying(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.PreserveName
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
- afterCreateObject(Point3i, Optional<Resolution>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
- aggEnd(Aggregator) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiver
- aggEnd(Aggregator) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
- aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
- aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
- aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
- aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
- aggEnd(Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
- AggIDCounter - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
- AggIDCounter(int) - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
- AggregateAnnotations<S extends AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
-
Aggregates many per-image annotations together in form of a CSV file.
- AggregateAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
- AggregateReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
- AggregateReceiverList<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
- AggregateReceiverList() - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
- aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
- aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MaxFeatureIntersectingObjects
- aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MinFeatureIntersectingObjectsAboveThreshold
- aggregateResults(List<Double>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjectsAboveThreshold
- AggregateTriggerBank<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
- AggregateTriggerBank(ExtractScoreSize<T>) - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
- Aggregator - Class in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
- Aggregator(int) - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- AggregatorException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
- AggregatorException() - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregatorException
- AggregatorException(Exception) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregatorException
- AggregatorException(String) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregatorException
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
- aggReport(Reporting<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
- aggReport(Reporting<T>, Aggregator) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiver
- aggReport(Reporting<T>, Aggregator) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
- aggStart(FeedbackBeginParameters<VoxelizedMarksWithEnergy>, Aggregator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
- aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiver
- aggStart(FeedbackBeginParameters<T>, Aggregator) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateReceiverList
- All - Class in org.anchoranalysis.io.output.bean.enabled
-
All outputs are allowed irrespective of
outputName. - All - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects all possible channels from all possible stacks
- All() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.All
- ALL_DIMENSIONS - org.anchoranalysis.image.voxel.object.morphological.SelectDimensions
-
The dilation applies in all dimensions (X, Y and Z)
- allChannelsHaveIdenticalType() - Method in class org.anchoranalysis.image.core.stack.Stack
-
Determines if all channels have an identical voxel data-type.
- allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.core.stack.Stack
-
Determines if all channels have a specific data-type.
- allChannelsHaveType(VoxelDataType) - Method in class org.anchoranalysis.image.core.stack.TimeSequence
- allFileTypes() - Method in class org.anchoranalysis.io.generator.ConcatenateFileTypes
- allHeaders() - Method in class org.anchoranalysis.feature.io.results.LabelHeaders
-
The non-group and group headers combined (in this order respectively)
- allLabels(NoSharedState) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
- allLabels(ImageCSVLabellerInitParams) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
- allLabels(ImageLabellerStringMapInitParams<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
- allLabels(T) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller
-
A set of identifiers for all groups that can be outputted by the labeller.
- allMatchIntensity(ObjectMask, Voxels<T>, IntPredicate) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
-
Do all points on an object-mask match a predicate on the point's voxel-intensity?
- allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Allocates a new buffer of unsigned-bytes.
- allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
-
Allocates a new (direct) buffer of unsigned-ints.
- allocate(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
Allocates a new (direct) buffer of unsigned-shorts.
- allocateBuffer() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
- allocateFloat(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
-
Allocates a new float voxel-buffers of given size.
- allocateFloatArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
-
Creates an array of float voxel-buffers of given size.
- allocateUnsignedByte(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
-
Allocates a new unsigned byte voxel-buffer of given size.
- allocateUnsignedByteArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
-
Creates an array of unsigned byte voxel-buffers of given size.
- allocateUnsignedInt(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
-
Allocates a new unsigned int voxel-buffers of given size.
- allocateUnsignedIntArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
-
Creates an array of unsigned int voxel-buffers of given size.
- allocateUnsignedShort(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
-
Allocates a new unsigned short voxel-buffers of given size.
- allocateUnsignedShortArray(int) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferFactory
-
Creates an array of unsigned short voxel-buffers of given size.
- AllowEmpty - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a String is allowed be empty, otherwise by default it must be non-empty.
- allSlices(Voxels<U>, Function<U, T>, Function<AbstractNativeImg<S, T>, S>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.Wrap
- AllSlicesMaskEverythingNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
-
Only takes pixels where indexNonZero has a nonzero pixel
- AllSlicesMaskEverythingNonZero() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
- AllSlicesMaskNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
-
Gets all slices where indexNonZero has at least one non-zero pixel in that slice
- AllSlicesMaskNonZero() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
- allSuccessful() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
-
Did all jobs execute and completely successfully?
- AllValuesOff - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
- AllValuesOff() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.AllValuesOff
- AllValuesOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
-
Creates a new mask of particular dimensionality where all values are ON
- AllValuesOn() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.AllValuesOn
- Always - Class in org.anchoranalysis.plugin.image.bean.object.match
-
Specifies a single object that will always be the "match" for whatever source object.
- Always() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Always
- ALWAYS_NEW - org.anchoranalysis.image.core.channel.convert.ConversionPolicy
- AlwaysAllowed - Class in org.anchoranalysis.io.output.writer
-
Allows every output, irrespective of whether the
OutputterCheckedallows the output-name. - AlwaysAllowed(OutputterChecked, Optional<WriterExecuteBeforeEveryOperation>) - Constructor for class org.anchoranalysis.io.output.writer.AlwaysAllowed
- alwaysExecuteBeforeCallingLibrary() - Static method in class org.anchoranalysis.plugin.opencv.CVInit
-
This routine must always be executed at least once before calling any routines in the OpenCV library
- AlwaysNew<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.strategy.replace
-
Always create a new session-input with no reuse or caching
- AlwaysNew(CacheCreator) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.AlwaysNew
-
Constructor with default means of creating a session-input
- AlwaysNew(CacheCreator, FindChildStrategy) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.AlwaysNew
- AnchorBean<F> - Class in org.anchoranalysis.bean
-
The base class of all beans used in Anchor.
- AnchorBean() - Constructor for class org.anchoranalysis.bean.AnchorBean
- AnchorBeanFactory - Class in org.anchoranalysis.bean.xml.factory
-
Base class for all Anchor-specific bean factories
- AnchorBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.AnchorBeanFactory
- AnchorCheckedException - Exception in org.anchoranalysis.core.exception
-
A base class for all checked exceptions used on the Anchor platform
- AnchorCheckedException() - Constructor for exception org.anchoranalysis.core.exception.AnchorCheckedException
- AnchorCheckedException(String) - Constructor for exception org.anchoranalysis.core.exception.AnchorCheckedException
- AnchorCheckedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.AnchorCheckedException
- AnchorCheckedException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.AnchorCheckedException
- AnchorCombinableException - Exception in org.anchoranalysis.core.exception.combinable
-
An exception that can be combined with similar exceptions and summarized.
- AnchorCombinableException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
- AnchorDefaultBeanFactory - Class in org.anchoranalysis.bean.xml.factory
-
The default bean factory used for initializing AnchorBeans
- AnchorDefaultBeanFactory(BeanInstanceMap) - Constructor for class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
- AnchorFriendlyCheckedException - Exception in org.anchoranalysis.core.exception.friendly
-
A base class for particular checked-exceptions which are guaranteed to provide a user-friendly error description.
- AnchorFriendlyCheckedException(String) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
-
A user-friendly error message WITHOUT a cause.
- AnchorFriendlyCheckedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
-
A user-friendly error message and its cause.
- AnchorFriendlyCheckedException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
-
A wrapped exception.
- AnchorFriendlyRuntimeException - Exception in org.anchoranalysis.core.exception.friendly
-
A base class for particular runtime-exceptions which are guaranteed to provide a user-friendly error description.
- AnchorFriendlyRuntimeException(String) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
-
A user-friendly error message WITHOUT a cause.
- AnchorFriendlyRuntimeException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
-
A user-friendly error message and its cause.
- AnchorFriendlyRuntimeException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
-
A wrapped exception.
- AnchorImpossibleSituationException - Exception in org.anchoranalysis.core.exception.friendly
-
A run-time exception to throw in situations which should never occur, instead of
- AnchorImpossibleSituationException() - Constructor for exception org.anchoranalysis.core.exception.friendly.AnchorImpossibleSituationException
- AnchorNeverOccursException - Exception in org.anchoranalysis.core.exception
-
This is an exceotion that should never be thrown, but can be used for type-safety where an exception is needed
- AnchorNeverOccursException() - Constructor for exception org.anchoranalysis.core.exception.AnchorNeverOccursException
- AnchorRuntimeException - Exception in org.anchoranalysis.core.exception
-
A base class for all unchecked (runtime) exceptions used on the Anchor platform
- AnchorRuntimeException() - Constructor for exception org.anchoranalysis.core.exception.AnchorRuntimeException
- AnchorRuntimeException(String) - Constructor for exception org.anchoranalysis.core.exception.AnchorRuntimeException
- AnchorRuntimeException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.AnchorRuntimeException
- AnchorRuntimeException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.AnchorRuntimeException
- And - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation and voxelwise on both masks, modifying {mask} with the result.
- And - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
-
Applies multiples filter with logical AND i.e.
- And() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.And
- And() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.And
- AndCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
-
Combines two UpdatableBeforeConditions as LOGICAL ANDs
- AndCondition(UpdatableBeforeCondition, UpdatableBeforeCondition) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
- AndKernel - Class in org.anchoranalysis.image.voxel.kernel
- AndKernel(BinaryKernel, BinaryKernel) - Constructor for class org.anchoranalysis.image.voxel.kernel.AndKernel
- AndList - Class in org.anchoranalysis.plugin.mpp.bean.check
- AndList() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.AndList
- AndObjectsWithMasks - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask
-
Reduce the size of individual objects (if neccessary, and minimally) to fit within a binary-mask.
- AndObjectsWithMasks() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
- AngleRotation - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
- AngleRotation() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
- AnisotropicDiffusion - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider
-
Perona-Malik Anisotropic Diffusion
- AnisotropicDiffusion() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
- AnnealScheme - Class in org.anchoranalysis.mpp.bean.anneal
- AnnealScheme() - Constructor for class org.anchoranalysis.mpp.bean.anneal.AnnealScheme
- Annotation - Interface in org.anchoranalysis.annotation
-
Base class for types of image annotations.
- AnnotationAggregateCSVGenerator - Class in org.anchoranalysis.plugin.annotation.bean.aggregate
- AnnotationAggregateCSVGenerator() - Constructor for class org.anchoranalysis.plugin.annotation.bean.aggregate.AnnotationAggregateCSVGenerator
- AnnotationBackground - Class in org.anchoranalysis.annotation.io.bean
- AnnotationBackground() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotationBackground
- AnnotationComparisonAssigner<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
- AnnotationComparisonAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner
- AnnotationComparisonInput<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.comparison
- AnnotationComparisonInput(T, Tuple2<Comparer, Comparer>, Tuple2<String, String>, StackReader) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
- AnnotationComparisonInputManager<T extends InputFromManager> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
- AnnotationComparisonInputManager() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- AnnotationDeleter - Interface in org.anchoranalysis.annotation.io
- annotationExistsCorrespondTo(Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationReader
- AnnotationGroup<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.comparison
- AnnotationGroup(String) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- AnnotationGroupList<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.comparison
- AnnotationGroupList() - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
- AnnotationGroupObject - Class in org.anchoranalysis.plugin.annotation.comparison
- AnnotationGroupObject(String) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
- AnnotationInputManager<T extends ProvidesStackInput,S extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io.bean
- AnnotationInputManager() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
- AnnotationLabel - Class in org.anchoranalysis.plugin.annotation.bean.label
- AnnotationLabel() - Constructor for class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
- annotationLabelFor(ProvidesStackInput) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
-
Returns a label describing the annotation, or empty() if this makes no sense
- annotationLabelFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
- annotationLabelFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
- AnnotationMarksComparer<T> - Class in org.anchoranalysis.plugin.annotation.bean.comparer
- AnnotationMarksComparer() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.AnnotationMarksComparer
- annotationPathFor(ProvidesStackInput) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
- annotationPathFor(ProvidesStackInput) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
- AnnotationReader<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
- AnnotationWithMarks - Interface in org.anchoranalysis.annotation.mark
-
An image-annotation that involves a mark-collection.
- AnnotationWithStrategy<T extends AnnotatorStrategy> - Class in org.anchoranalysis.annotation.io
-
An annotation that has been combined with its strategy.
- AnnotationWithStrategy(ProvidesStackInput, T) - Constructor for class org.anchoranalysis.annotation.io.AnnotationWithStrategy
- AnnotationWriter<T extends Annotation> - Interface in org.anchoranalysis.annotation.io
- AnnotatorStrategy - Class in org.anchoranalysis.annotation.io.bean
- AnnotatorStrategy() - Constructor for class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
- Anonymize - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
-
Copies files to a number 001 002 etc.
- Anonymize() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
- any() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
-
Returns voxels that are not cast to any specific buffer type
- anyDimensionIsLargerThan(Extent) - Method in class org.anchoranalysis.spatial.Extent
-
Returns true if any dimension in this extent is larger than the corresponding dimension in
otherextent - anyExists() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
- anyExists() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
- anyExists() - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate
-
Does at least one value satisfy the predicate - across all voxels?
- anyMatch(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Does the predicate evaluate to true on any object in the collection?
- anyPredicateMatch(Voxels<T>, Predicate<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
-
Tries to apply a predicate to all the remaining buffer locations, returning true if the predicate matches.
- AnySliceCenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
-
The center ps of at least one slice should be on the stack Tries overall center point first, and then projects it onto each slice
- AnySliceCenterOnMask() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.AnySliceCenterOnMask
- append(Optional<FeatureList<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
-
Appends one or more additional (optional) feature-lists
- AppendCsv - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
A CSV that is appended from the root of a project
- AppendCsv() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendCsv
- AppendFilePath - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
- AppendFilePath() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendFilePath
- AppendHistogram - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
- AppendHistogram() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
- AppendKeyValueParams - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
- AppendKeyValueParams() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
- AppendMarks - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
- AppendMarks() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendMarks
- AppendObjects - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
- AppendObjects() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendObjects
- AppendStack - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
A stack from a stack-collection
- AppendStack() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
- AppendStackDirect - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
A stack from a stack-collection
- AppendStackDirect() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
- apply(int) - Method in interface org.anchoranalysis.core.functional.checked.CheckedIntFunction
-
Calls the function
- apply(int, int) - Method in interface org.anchoranalysis.core.functional.checked.IntBinaryOperation
- apply(Integer) - Method in class org.anchoranalysis.core.index.IndexBridge
- apply(String, Path) - Static method in class org.anchoranalysis.io.generator.text.WriteStringToFile
- apply(Throwable, Writer, String, int, boolean) - Static method in class org.anchoranalysis.core.exception.friendly.RecursivelyDescribeExceptionStack
-
Incrementally adds a line to a string builder with the message of each exception moving onto the next nested exception until there are no more
- apply(IFormatReader, ReadOptions, int) - Method in class org.anchoranalysis.io.bioformats.DimensionsCreator
- apply(ImageInitParams) - Static method in class org.anchoranalysis.image.bean.nonbean.init.CreateCombinedStack
- apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskAnd
-
Performs a AND operation on each voxel in two masks, writing the result onto the second mask.
- apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskIfHighLow
-
Performs a
iff first==HIGH and second==LOW then LOWoperation on each voxel in two masks, writing the result onto the second mask. - apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskOr
-
Performs a OR operation on each voxel in two masks, writing the result onto the first mask.
- apply(Mask, Mask) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskXor
-
Performs a XOR (exclusive OR) operation on each voxel in two masks, writing the result onto the first mask.
- apply(BinaryKernel, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
- apply(BinaryKernel, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
- apply(ObjectMask, double, int, int) - Static method in class org.anchoranalysis.plugin.points.bean.contour.SplitContourSmoothingSpline
-
1.
- apply(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, BinaryValuesByte, BinaryValuesByte) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskAnd
-
Performs a AND operation on each voxel in two
Voxels(considered to be masks), writing the result onto the second mask. - apply(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, BinaryValuesByte, BinaryValuesByte) - Static method in class org.anchoranalysis.image.core.mask.combine.MaskXor
-
Performs a XOR (exclusive OR) operation on each voxel in two
Voxels(considered to be masks), writing the result onto the second mask. - apply(S) - Method in interface org.anchoranalysis.core.functional.checked.CheckedFunction
-
Calls the function
- apply(S, T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedBiFunction
-
Calls the function
- apply(T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedUnaryOperator
- applyAsDouble(T, U) - Method in interface org.anchoranalysis.core.functional.checked.CheckedToDoubleBiFunction
-
Applies this function to the given arguments.
- applyAsInt(S) - Method in interface org.anchoranalysis.core.functional.checked.CheckedToIntFunction
-
Calls the function
- applyCoefficientsToMark(DoubleMatrix2D, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
- applyDelta(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta
-
Applies the changes to enable or disable additional outputs, if they are defined.
- applyFitResultToMark(Ellipsoid, Dimensions, double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- applyForCount(BinaryKernel, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
- applyForCount(CountKernel, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
-
Applies the kernel to voxels and sums the returned value
- applyForCount(CountKernel, Voxels<UnsignedByteBuffer>, BoundingBox) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
-
Applies the kernel to voxels and sums the returned value
- applyForCountOnMask(BinaryKernel, Voxels<UnsignedByteBuffer>, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
- applyGlobal(List<Point3i>) - Method in class org.anchoranalysis.image.core.outline.traverser.OutlineTraverser
-
Root point is arbitrarily chosen from object
- applyGlobal(Point3i, List<Point3i>) - Method in class org.anchoranalysis.image.core.outline.traverser.OutlineTraverser
- ApplyImageJMorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.mask
-
Applies an ImageJ (2D) morphological operation to voxels
- applyInitializationIfPossibleTo(Object, Object, Logger) - Method in class org.anchoranalysis.bean.initializable.property.PropertyInitializer
-
Applies the initialization to a property using the current or extracted params if possible.
- ApplyKernel - Class in org.anchoranalysis.image.voxel.kernel
-
Applies a kernel to a Voxel Box
- applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
- applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
- applyMorphologicalOperation(Mask, boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
- applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
- applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
- applyMorphologicalOperation(ObjectMask, Optional<Extent>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
- applyOperation(Dimensions, UnaryOperator<Stack>) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
-
Applies an operation on each stack in the collection and returns a new derived collection
- applyOperation(BinaryVoxels<UnsignedByteBuffer>, String, int) - Static method in class org.anchoranalysis.plugin.imagej.mask.ApplyImageJMorphologicalOperation
- applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
- applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
- applyOperation(ObjectMask, Extent, boolean) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
- ApplyPermutations<T extends AnchorBean<T>> - Class in org.anchoranalysis.bean.permute
-
Applies a
PermutePropertyto a bean to create new duplicated beans each with a permutation - ApplyPermutations(ApplyPermutations.NameGetter<T>, ApplyPermutations.NameSetter<T>) - Constructor for class org.anchoranalysis.bean.permute.ApplyPermutations
- ApplyPermutations.NameGetter<S> - Interface in org.anchoranalysis.bean.permute
- ApplyPermutations.NameSetter<S> - Interface in org.anchoranalysis.bean.permute
- applyPermutationsToCreateDuplicates(List<T>, PermuteProperty<S>, PermutationSetter) - Method in class org.anchoranalysis.bean.permute.ApplyPermutations
-
Takes a list of beans, and creates a permuted version, updating the custom names
- applyRadiiSubtractScale(double, double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- applyRankFilter(Channel, int, int) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper
-
Applies a 2D rank-filter to each slice independently.
- ApplyRegExSubstitution - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
-
A regular expression substitution (replaceAll) is applied to the relative-path
- ApplyRegExSubstitution() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.ApplyRegExSubstitution
- applyStrategy(MergeCandidate) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeStrategy
- applyUntilPositive(CountKernel, Voxels<UnsignedByteBuffer>, BoundingBox) - Static method in class org.anchoranalysis.image.voxel.kernel.ApplyKernel
-
Applies the kernel to voxels until a positive value is returned, then exits with true
- ArbitraryInsidePoint - Class in org.anchoranalysis.plugin.image.feature.bean.object.single
-
Calculates deterministicly a point that is definitely inside the object-mask.
- ArbitraryInsidePoint() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
- ArbitraryInsidePoint(String) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
- ArbitraryPointCommon - Class in org.anchoranalysis.mpp.feature.addcriteria
-
If one arbitrarily point overlaps between two MarkPointList then true, otherwise false
- ArbitraryPointCommon() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
- Area<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
-
Area of the stack (XY dimensions only, Z dimension is not considered)
- Area() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Area
- areAllPointsInBigNeighborhood(List<Point3i>) - Static method in class org.anchoranalysis.image.core.points.PointsNeighborChecker
-
Are all points in a list neighboring the next point in the list?
- AreaPhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.area
-
Area expressed in physical coordinates
- AreaPhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
- AreaPixels - Class in org.anchoranalysis.image.bean.unitvalue.extent.area
-
Area expressed as square pixels
- AreaPixels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
- AreaPixels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
- areEqual(double, double) - Static method in class org.anchoranalysis.math.arithmetic.DoubleUtilities
-
Are the two numbers equal?
- areEqual(float, float) - Static method in class org.anchoranalysis.math.arithmetic.FloatUtilities
-
Are the two numbers equal?
- areNeighborsDistinct(List<Point3i>) - Static method in class org.anchoranalysis.image.core.points.PointsNeighborChecker
-
Makes sure no successive neighbors are equal
- arePointsNeighbors(Point3i, Point3i) - Static method in class org.anchoranalysis.image.core.points.PointsNeighborChecker
- areXmlEqual(Document, Document) - Static method in class org.anchoranalysis.test.TestLoader
-
Does a check if the XML documents are equal
- ArgumentConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path
-
Converts string passed as arguments.
- arithmetic() - Method in class org.anchoranalysis.image.core.channel.Channel
- arithmetic() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
- arithmetic() - Method in class org.anchoranalysis.image.voxel.Voxels
-
Methods to manipulate the voxel-values via arithmetic
- arithmetic() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- ArithmeticWithConstantBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Base-class for operations that perform a binary arithmetic operation with each voxel-value and a constant.
- ArithmeticWithConstantBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase
- ArithmeticWithConstantConditionallyWriteBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
- ArithmeticWithConstantConditionallyWriteBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase
- ArrangeRaster - Class in org.anchoranalysis.image.bean.provider.stack
-
Creates a stack that tiles (or otherwise combines) other providers
- ArrangeRaster() - Constructor for class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
- ArrangeStack - Interface in org.anchoranalysis.image.bean.nonbean.spatial.arrange
- ArrangeStackBean - Class in org.anchoranalysis.image.bean.spatial.arrange
- ArrangeStackBean() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.ArrangeStackBean
- ArrangeStackException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange
- ArrangeStackException(Exception) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStackException
- ArrangeStackException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStackException
- array() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
The array of the buffer ala
ByteBuffer.array(). - array() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
The array of the buffer ala
ShortBuffer.array(). - asByte() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- asByte(ImageProcessor) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToVoxelBuffer
-
Convert a
ImageProcessortoVoxelBuffer<UnsignedByteBuffer> - asByteOrCreateEmpty(boolean) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
-
Reuses the existing buffer if byte, otherwise creates a new empty byte buffer
- AsCollection - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
- AsCollection() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.AsCollection
- asCollectionOrderNotPreserved() - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements
-
Returns the scaled-elements as a collection but without preserving the original element order.
- asExtent() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
-
Creates an extent with identical width and height and depth (z-extent) of 1
- asExtent(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
-
Creates an extent with identical width and height and a specific depth (z-extent)
- asFloat() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- asInt() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- asList() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- asList() - Method in class org.anchoranalysis.feature.name.FeatureNameList
- asList() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
-
Exposes the underlying objects as a list
- asList() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- asList() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
- asListChannels() - Method in class org.anchoranalysis.image.core.stack.Stack
- asListOrderPreserved(List<T>) - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements
-
Returns a list of scaled-elements corresponding to a list of unscaled-elements
- asMap() - Method in class org.anchoranalysis.core.identifier.name.MapCreate
- AsMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
- AsMark() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsMark
- asMarks() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
- AsObject - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
- AsObject() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
- AsObjectMask - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
-
Treats a channel as an object-mask, assuming binary values of 0 and 255 and calls an object-mask feature
- AsObjectMask() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
- asObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
- asOperationFailedException() - Method in exception org.anchoranalysis.core.index.GetOperationFailedException
- asOrderedArray() - Method in class org.anchoranalysis.spatial.Extent
- asPath() - Method in class org.anchoranalysis.bean.shared.path.RootPath
- asPoint() - Method in class org.anchoranalysis.image.bean.spatial.Padding
- assertCalc(ResultsVector, Object...) - Static method in class org.anchoranalysis.test.feature.plugins.ResultsVectorTestUtilities
- assertDoubleResult(String, Feature<T>, T, double) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator
- assertDoubleResult(String, Feature<T>, T, Optional<SharedObjects>, double) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator
- assertDoubleResult(String, Feature<T>, T, T, double, double) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculatorDuo
- assertIntResult(String, Feature<T>, T, int) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator
- assertIntResult(String, Feature<T>, T, Optional<SharedObjects>, int) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculator
- assertIntResult(String, Feature<T>, T, T, int, int) - Static method in class org.anchoranalysis.test.feature.plugins.FeatureTestCalculatorDuo
- assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- assertValid() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
- assertValid() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
- asShort() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- asShort(ImageProcessor) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToVoxelBuffer
-
Convert a
ImageProcessortoVoxelBuffer<UnsignedShortBuffer> - assignAccepted(DualMarks) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
-
Assigns marks with an overall accepted state.
- assignBestFromCurrent() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
- assignBoundingBox(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundedList
-
Assigns a new containing bounding-box.
- assignBoundingBoxAndMap(BoundingBox, UnaryOperator<T>) - Method in class org.anchoranalysis.spatial.box.BoundedList
-
Assigns a new containing bounding-box and maps each individual element.
- assignCurrent(Optional<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
- assignDescription(ManifestDirectoryDescription) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
-
Assigns a description, which may not already exist.
- assignEachMatchingPoint(Voxels<?>, IntPredicate, int) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
-
Assigns a value to any voxel whose intensity matches a predicate, reading and writing the buffer as an
int. - assignFrom(CachedSupplierBase<T>) - Method in class org.anchoranalysis.core.cache.CachedSupplierBase
- assignFrom(Mark) - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
-
Assigns a new mark to replace the existing mark.
- AssignFromChannel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
Copies the pixels from
channelAssignFromtochannel(possibly masking) - AssignFromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
- AssignFromIntersectingObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
Matches source-objects to target objects, based upon intersection, and assigns the value in the respective source object to the target object
- AssignFromIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
- AssignFromParams - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
- AssignFromParams() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
- assignFunction(String) - Method in class org.anchoranalysis.io.manifest.ManifestDescription
-
Assigns a new function.
- assignMaximumIndex(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
- assignMaximumIndex(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
- assignMaximumIndex(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
-
If the sequence-type supports a different maximum-index to that derived from the elements
SequenceType.update(T), this assigns it. - assignMaximumIndex(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
- Assignment - Interface in org.anchoranalysis.annotation.io.assignment
- AssignmentGenerator - Class in org.anchoranalysis.annotation.io.assignment.generator
-
Outputs a raster showing an
Assignmenton a background. - AssignmentGenerator(DisplayStack, IntFunction<ColorPool>, boolean, Tuple2<String, String>, boolean, int) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
- AssignmentMaskIntersection - Class in org.anchoranalysis.annotation.io.assignment
-
Calculates statistics (DICE, Jaccard etc.) based upon corresponding two object-masks
- AssignmentMaskIntersection(ObjectMask, ObjectMask) - Constructor for class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
- AssignmentObjectFactory - Class in org.anchoranalysis.annotation.io.assignment
- AssignmentObjectFactory(FeatureEvaluator<FeatureInputPairObjects>, boolean) - Constructor for class org.anchoranalysis.annotation.io.assignment.AssignmentObjectFactory
- AssignmentOverlapFromPairs - Class in org.anchoranalysis.annotation.io.assignment
-
Pairs objects in left with objects in right
- AssignmentOverlapFromPairs() - Constructor for class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- AssignMode<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
-
How assignments and other decisions are made in the SimulatedAnnealing optimizaton
- AssignMode() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
- assignOff() - Method in class org.anchoranalysis.image.core.mask.Mask
- assignOff() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- assignOff() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Assigns OFF value to voxels, expecting global coordinates
- assignOn() - Method in class org.anchoranalysis.image.core.mask.Mask
- assignOn() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- assignOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Assigns ON value to voxels, expecting global coordinates
- assignParentFolder(Optional<MutableDirectory>) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
- assignPath(Path) - Method in class org.anchoranalysis.io.manifest.directory.SubdirectoryBase
- assignPaused(DualMarks) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
-
Assigns marks with an overall paused state.
- assignPriority(ObjectVertex, ObjectVertex, GraphLogger) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority
-
Assigns a priority to a potential merge
- AssignPriority - Class in org.anchoranalysis.plugin.image.object.merge.priority
- AssignPriority() - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority
- AssignPriorityFromImprovement - Class in org.anchoranalysis.plugin.image.object.merge.priority
-
Allows merges if there is an increase in the payload i.e.
- AssignPriorityFromImprovement(PayloadCalculator) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromImprovement
- AssignPriorityFromPair - Class in org.anchoranalysis.plugin.image.object.merge.priority
-
Calculates pair-feature on each potential merge, and this value determines priority..
- AssignPriorityFromPair(FeatureCalculatorSingle<FeatureInputPairObjects>, double, RelationToValue) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromPair
- assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriority
- assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromImprovement
- assignPriorityToEdge(ObjectVertex, ObjectVertex, ObjectMask, ErrorReporter) - Method in class org.anchoranalysis.plugin.image.object.merge.priority.AssignPriorityFromPair
- assignProposal(Optional<T>, KernelWithIdentifier<S>) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- assignProposal(OptimizationStep<S, T>, TransformationContext, KernelWithIdentifier<S>) - Method in interface org.anchoranalysis.mpp.segment.kernel.KernelAssigner
- assignProposal(OptimizationStep<S, T>, TransformationContext, KernelWithIdentifier<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.kernel.assigner.KernelAssignerAddErrorLevel
- assignProposal(OptimizationStep<S, T>, TransformationContext, KernelWithIdentifier<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.kernel.assigner.KernelAssignerCalculateEnergyFromKernel
- assignRejected(DualMarks, T) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
-
Assigns marks with an overall rejected state.
- assignType(String) - Method in class org.anchoranalysis.io.manifest.ManifestDescription
-
Assigns a new type.
- assignValue(int) - Method in class org.anchoranalysis.image.core.channel.Channel
- assignValue(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
Assigns a value to a bounded-voxels accepting global coordinates for objects, boxes etc.
- assignValue(int) - Method in class org.anchoranalysis.image.voxel.Voxels
-
Provides a means to assign a constant-value to some or all of the voxels
- assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsAsFloat
- assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsAsInt
- assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsAsShort
- assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
- assignValue(int) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- AssignValue - Class in org.anchoranalysis.plugin.image.bean.channel.provider.assign
-
Assigns a constant (scalar) value to the portion of the image covered by a mask
- AssignValue() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
- AsSingle - Class in org.anchoranalysis.mpp.feature.bean.energy.element
-
Extracts one of the memos from the pair, and processes as a
FeatureSingleMemo - AsSingle() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
- AsSingleMark - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
- AsSingleMark() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.AsSingleMark
- associatedFile() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
- associateXml(XMLConfiguration) - Method in interface org.anchoranalysis.bean.xml.AssociateXmlUponLoad
-
Associated
- associateXml(XMLConfiguration) - Method in class org.anchoranalysis.experiment.bean.Experiment
- associateXml(XMLConfiguration) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- AssociateXmlUponLoad - Interface in org.anchoranalysis.bean.xml
-
For classes that wish to have a XmlConfiguration associated with them
- asStack() - Method in class org.anchoranalysis.feature.energy.EnergyStack
- asStack() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
- asStack() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- asTuple() - Method in class org.anchoranalysis.spatial.Extent
-
Exposes the extent as a tuple.
- asVoxels() - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBuffer
-
The target buffer
- atanHandlingNan(double) - Static method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
- atBorder(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
- AtBorderBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
- AtBorderBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
- atBorderXY(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
- AtBorderXY - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
- AtBorderXY() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderXY
- atBorderZ(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
- AtBorderZ - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
- AtBorderZ() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderZ
- atCorner(ReadableTuple3i, VoxelsExtracter<T>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory
-
Projects a
VoxelsExtracterto a corner in a larger global space - AtIndex - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Creates a new object-collection with only a single element (at a particular index) in the existing collection.
- AtIndex() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
- AtLeastZSlices - Class in org.anchoranalysis.plugin.io.bean.groupfiles.check
- AtLeastZSlices() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.check.AtLeastZSlices
- AtScale - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Perform a segmentation at a different scale, and then fit the results back to the original scale.
- AtScale() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
- attachObject(Channel) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
- attachObject(Histogram) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
- attachObject(Histogram) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
- attachObject(Histogram) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
- attachObject(S) - Method in interface org.anchoranalysis.image.core.channel.convert.attached.ChannelConverterAttached
- AutoLocalThreshold - Class in org.anchoranalysis.plugin.fiji.bean.mask.provider
-
Applies local thresholding algorithm using Fiji's {link Auto_Local_Threshold} plugin
- AutoLocalThreshold() - Constructor for class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
- Autoname - Class in org.anchoranalysis.plugin.io.bean.channel.map
-
Names of the channels from the metadata if it exists, or after RGB, or by index
- Autoname() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.Autoname
- AxisAlignedUnitVector - Class in org.anchoranalysis.image.bean.spatial.direction
- AxisAlignedUnitVector() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
- AxisLimits - Class in org.anchoranalysis.plot
- AxisLimits() - Constructor for class org.anchoranalysis.plot.AxisLimits
- AxisLimits(double, double) - Constructor for class org.anchoranalysis.plot.AxisLimits
- AxisRatioEllipsoid - Class in org.anchoranalysis.plugin.points.bean.feature.object.conic
- AxisRatioEllipsoid() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.object.conic.AxisRatioEllipsoid
- AxisType - Enum in org.anchoranalysis.spatial.axis
- AxisTypeConverter - Class in org.anchoranalysis.spatial.axis
-
Converts to/from
AxisTypeto string representations and integer index (0 for X, 1 for Y, 2 for Z) - AxisTypeException - Exception in org.anchoranalysis.spatial.axis
- AxisTypeException(String) - Constructor for exception org.anchoranalysis.spatial.axis.AxisTypeException
B
- background() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
- background(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksFlattenedGenerator
- background(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGenerator
- background(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
- BackgroundCreator - Class in org.anchoranalysis.mpp.io.output
- backgroundStack() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- BackgroundSubtractor - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider
- BackgroundSubtractor() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor
- BarPlot<T> - Class in org.anchoranalysis.plot.index
-
A bar plot, stacked or non-stacked.
- BarPlot(String, String[], GetForSeries<T, String>, GetForSeries<T, Double>, GetForSeries<T, Paint>, boolean) - Constructor for class org.anchoranalysis.plot.index.BarPlot
- Base<T> - Class in org.anchoranalysis.image.voxel.extracter
- Base(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.extracter.Base
- BASE - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
- BBoxRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
- BBoxRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.BBoxRatio
- BeanDuplicateException - Exception in org.anchoranalysis.bean.error
-
An exception occurs when the duplication of a bean fails
- BeanDuplicateException(Exception) - Constructor for exception org.anchoranalysis.bean.error.BeanDuplicateException
- BeanDuplicateException(String) - Constructor for exception org.anchoranalysis.bean.error.BeanDuplicateException
- BeanDuplicateException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.error.BeanDuplicateException
- BeanField - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a field in an Anchor Bean class is to be treated as a bean-field.
- beanFor(Field, AnchorBean<?>) - Static method in class org.anchoranalysis.bean.permute.setter.PermutationSetterUtilities
-
Finds a bean corresponding to a field (exceptionally handling a List by taking the first item in it)
- BeanInitParams - Interface in org.anchoranalysis.bean.initializable.params
-
Parent class for all parameters used to initialise beans in
InitializableBean - BeanInstanceMap - Class in org.anchoranalysis.bean
-
Maps a
AnchorBeanfamily-type to some beans belong to the family. - BeanInstanceMap() - Constructor for class org.anchoranalysis.bean.BeanInstanceMap
- BeanMisconfiguredException - Exception in org.anchoranalysis.bean.error
-
If a Bean is misconfigured
- BeanMisconfiguredException(String) - Constructor for exception org.anchoranalysis.bean.error.BeanMisconfiguredException
- BeanMisconfiguredException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.error.BeanMisconfiguredException
- BeanMisconfiguredXmlException - Exception in org.anchoranalysis.bean.xml.error
-
A bean's XML is thrown when a bean has misconfigured XML
- BeanMisconfiguredXmlException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
-
Constructor
- BeanMisconfiguredXmlException(Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
-
Constructor
- BeanPathUtilities - Class in org.anchoranalysis.bean.xml.factory
- BeanProviderAsStackBase<T,S> - Class in org.anchoranalysis.image.bean.provider
-
A provider base-class that as well as providing type S, also provide a stack
- BeanProviderAsStackBase() - Constructor for class org.anchoranalysis.image.bean.provider.BeanProviderAsStackBase
- BeanStoreAdder - Class in org.anchoranalysis.bean.store
- BeanStrangeException - Exception in org.anchoranalysis.bean.error
-
When something quite strange happens that we don't usually want to catch.
- BeanStrangeException(String) - Constructor for exception org.anchoranalysis.bean.error.BeanStrangeException
- BeanStrangeException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.error.BeanStrangeException
- BeanTestChecker - Class in org.anchoranalysis.test.experiment
-
Checks to see if a bean has been misconfigured, when created manually in tests (thereby skipping the usual checks during the BeanXML loading process).
- BeanXmlException - Exception in org.anchoranalysis.bean.xml.error
-
An exception that occurs when one cannot process BeanXML for some reason
- BeanXmlException(String) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanXmlException
- BeanXmlException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanXmlException
- BeanXmlException(Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.BeanXmlException
- BeanXmlLoader - Class in org.anchoranalysis.bean.xml
-
Creates beans based on XML specifying their properties (including nested children).
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.task.Task
-
Called once before all calls to
Task.executeJob(org.anchoranalysis.experiment.task.ParametersUnbound<T, S>). - beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.task.TaskWithoutSharedState
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
- beforeAnyJobIsExecuted(Outputter, ConcurrencyPlan, ParametersExperiment) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
- beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.feature.bean.Feature
-
Dummy method, that children can optionally override
- beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
- beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
- beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
- beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
- beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
- beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
- beforeCalc(FeatureInitParams) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
- beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
- beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
- beforeCalcSetup(Histogram, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
- beforeCalcWithImageInitParams(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
- beforeCalcWithImageInitParams(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
- beforeCalcWithImageInitParams(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
- BeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
- beforeCopying(Path, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
- beforeCopying(Path, int) - Method in interface org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNaming
- beforeCopying(Path, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
- beforeCopying(Path, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.PreserveName
- beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
- beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
- beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
- beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
- beforeCreateObject(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
- BidirectionalBound - Class in org.anchoranalysis.mpp.bound
- BidirectionalBound(Optional<ResolvedBound>, Optional<ResolvedBound>) - Constructor for class org.anchoranalysis.mpp.bound.BidirectionalBound
- BinaryClassifierImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
- BinaryClassifierImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
- BinaryKernel - Class in org.anchoranalysis.image.voxel.kernel
- BinaryKernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.BinaryKernel
- BinaryKernelMorph3 - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
- BinaryKernelMorph3(BinaryValuesByte, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
- BinaryKernelMorph3Extent - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
- BinaryKernelMorph3Extent(BinaryValuesByte, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3Extent
- BinaryNotOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation
-
Selects anything that is not off voxels from a binary mask.
- BinaryNotOffVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
- BinaryNotOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation
-
Selects anything that is not on voxels from a binary mask.
- BinaryNotOnVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
- BinaryOffVoxels - Class in org.anchoranalysis.image.bean.threshold.relation
-
Selects only the off voxels from a binary mask.
- BinaryOffVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
- BinaryOnOffSetter - Interface in org.anchoranalysis.image.voxel.binary
- BinaryOnVoxels - Class in org.anchoranalysis.image.bean.threshold.relation
-
Selects only the on pixels from a binary mask.
- BinaryOnVoxels() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
- binaryOperation(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, IntBinaryOperation) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
-
Iterate over each voxel in a bounding-box - applying a binary operation with values from two input
Voxels<UnsignedByteBuffer>for each slice and writing it into an outputVoxels<UnsignedByteBuffer>. - BinaryOutcomeImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
- BinaryOutcomeImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
- binaryResizing(int) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorFactory
- BinarySegmentation - Class in org.anchoranalysis.image.bean.segment.binary
- BinarySegmentation() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentation
- BinarySegmentationOne - Class in org.anchoranalysis.image.bean.segment.binary
- BinarySegmentationOne() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
- BinarySegmentationParameters - Class in org.anchoranalysis.image.bean.nonbean.segment
-
Parameters that are optionally associated with a
BinarySegmentation - BinarySegmentationParameters() - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
- BinarySegmentationParameters(Optional<Resolution>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
- BinarySegmentationParameters(Optional<Histogram>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
- BinarySegmentationParameters(Resolution, Optional<Histogram>) - Constructor for class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
-
Constructor
- BinarySegmentationReference - Class in org.anchoranalysis.image.bean.segment.binary
- BinarySegmentationReference() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
- binarySegmentations() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- BinarySegmentationThreshold - Class in org.anchoranalysis.image.bean.segment.binary
- BinarySegmentationThreshold() - Constructor for class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
- BinarySegmentByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Performs a binary-segmentation using the upstream objects as masks.
- BinarySegmentByObject() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
- binaryValues() - Method in class org.anchoranalysis.image.core.mask.Mask
- binaryValues() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
-
Which two intensity values represent OFF and ON states
- binaryValues() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- BinaryValues - Class in org.anchoranalysis.image.voxel.binary.values
-
Two values representing
intbinary states in an unsigned-byte buffer e.g. - BinaryValues(int, int) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValues
- binaryValuesByte() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- BinaryValuesByte - Class in org.anchoranalysis.image.voxel.binary.values
-
Two values representing
bytebinary states in an unsigned-byte buffer e.g. - BinaryValuesByte(byte, byte) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
- BinaryValuesByte(int, int) - Constructor for class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
- binaryVoxels() - Method in class org.anchoranalysis.image.core.mask.Mask
- binaryVoxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- BinaryVoxels<T> - Class in org.anchoranalysis.image.voxel.binary
-
Like
Voxelsbut should only contain two distinct intensity-values representing ON and OFF states. - BinaryVoxels(Voxels<T>, BinaryValues) - Constructor for class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- BinaryVoxelsBase - Class in org.anchoranalysis.image.bean.threshold.relation
- BinaryVoxelsBase() - Constructor for class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
- BinaryVoxelsFactory - Class in org.anchoranalysis.image.voxel.binary
- binaryVoxelsFor(Voxels<T>, BinaryValues) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- bind(FeatureList<T>, FeatureInitParams, SharedFeatureMulti, Logger) - Method in class org.anchoranalysis.feature.session.strategy.replace.bind.BoundReplaceStrategy
- BindFailedException - Exception in org.anchoranalysis.io.output.outputter
- BindFailedException(String) - Constructor for exception org.anchoranalysis.io.output.outputter.BindFailedException
- BindFailedException(Throwable) - Constructor for exception org.anchoranalysis.io.output.outputter.BindFailedException
- BioformatsOpenedRaster - Class in org.anchoranalysis.io.bioformats
- BioformatsOpenedRaster(IFormatReader, IMetadata, ReadOptions) - Constructor for class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
- BioformatsReader - Class in org.anchoranalysis.io.bioformats.bean
- BioformatsReader() - Constructor for class org.anchoranalysis.io.bioformats.bean.BioformatsReader
- BioformatsReader(ReadOptions) - Constructor for class org.anchoranalysis.io.bioformats.bean.BioformatsReader
- BioformatsWriter - Class in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
-
Base class for writing a stack to the filesystem using the Bioformats library.
- BioformatsWriter() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.BioformatsWriter
- bitDepth() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
- bitDepth() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
- BitDepth - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
- BitDepth() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
- BlackBackgroud - Class in org.anchoranalysis.plot.bean.colorscheme
-
A black background and white axes.
- BlackBackgroud() - Constructor for class org.anchoranalysis.plot.bean.colorscheme.BlackBackgroud
- blockUntilLoaded() - Static method in class org.anchoranalysis.plugin.opencv.CVInit
-
Blocks a thread until the initialization has completed.
- blue() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- blur(VoxelsWrapper, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurGaussian3D
- blur(VoxelsWrapper, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurGaussianEachSlice2D
- blur(VoxelsWrapper, Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
- Blur - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Blurs an image using a particular strategy (defaults to a gaussian blur in each slice)
- Blur() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
- BlurGaussian3D - Class in org.anchoranalysis.plugin.image.bean.blur
-
Performs a Gaussian Blur in 3D
- BlurGaussian3D() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurGaussian3D
- BlurGaussianEachSlice2D - Class in org.anchoranalysis.plugin.image.bean.blur
-
Performs a Gaussian-blur in 2D on each slice independently
- BlurGaussianEachSlice2D() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurGaussianEachSlice2D
- BlurStrategy - Class in org.anchoranalysis.plugin.image.bean.blur
-
A method for applying blurring to an image
- BlurStrategy() - Constructor for class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
- bothNameAndParams() - Static method in class org.anchoranalysis.feature.list.NamedFeatureStoreFactory
- Bound - Class in org.anchoranalysis.mpp.bean.bound
- Bound() - Constructor for class org.anchoranalysis.mpp.bean.bound.Bound
- boundaryMax(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
- boundaryMax(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
-
Boundary to define the maximum accepted value in the range
- boundaryMax(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
- boundaryMin(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
- boundaryMin(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
-
Boundary to define the minimum accepted value in the range
- boundaryMin(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
- BoundCalculator - Class in org.anchoranalysis.mpp.bean.bound
- BoundCalculator() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundCalculator
- BoundCalculatorException - Exception in org.anchoranalysis.mpp.bound
- BoundCalculatorException(Exception) - Constructor for exception org.anchoranalysis.mpp.bound.BoundCalculatorException
- BoundCalculatorException(String) - Constructor for exception org.anchoranalysis.mpp.bound.BoundCalculatorException
- boundChanged(BoundChangeEvent) - Method in interface org.anchoranalysis.core.index.bounded.BoundChangeListener
- BoundChangeEvent - Class in org.anchoranalysis.core.index.bounded
- BoundChangeEvent(Object, BoundChangeEvent.BoundType) - Constructor for class org.anchoranalysis.core.index.bounded.BoundChangeEvent
- BoundChangeEvent.BoundType - Enum in org.anchoranalysis.core.index.bounded
- BoundChangeListener - Interface in org.anchoranalysis.core.index.bounded
- BoundDegrees - Class in org.anchoranalysis.mpp.bean.bound
- BoundDegrees() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundDegrees
- BoundDegrees(BoundDegrees) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundDegrees
- BoundedIndexContainer<T> - Interface in org.anchoranalysis.core.index.bounded
- BoundedIndexContainerBridge<H,S,E extends Exception> - Class in org.anchoranalysis.core.index.bounded.bridge
-
Bridges calls from hidden-type to external-type.
- BoundedIndexContainerBridge(BoundedIndexContainer<H>) - Constructor for class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
- BoundedIndexContainerBridgeWithIndex<H,S,E extends Exception> - Class in org.anchoranalysis.core.index.bounded.bridge
-
Bridges calls from hidden-type to external-type.
- BoundedIndexContainerBridgeWithIndex(BoundedIndexContainer<H>, BridgeElementWithIndex<H, S, E>) - Constructor for class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridgeWithIndex
- BoundedIndexContainerBridgeWithoutIndex<H,S,E extends Exception> - Class in org.anchoranalysis.core.index.bounded.bridge
-
Bridges calls from hidden-type to external-type.
- BoundedIndexContainerBridgeWithoutIndex(BoundedIndexContainer<H>, CheckedFunction<H, S, E>) - Constructor for class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridgeWithoutIndex
- BoundedIndexContainerFromList<T> - Class in org.anchoranalysis.core.index.bounded
- BoundedIndexContainerFromList(List<T>) - Constructor for class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
- BoundedList<T> - Class in org.anchoranalysis.spatial.box
-
One or more elements, each with an individual bounding-box, and collectively with a bounding-box that fully contains them all.
- BoundedRange - Interface in org.anchoranalysis.core.index.bounded
- BoundedRangeIncomplete - Interface in org.anchoranalysis.core.index.bounded
-
A range of discrete integers that is not complete (missing many integers).
- BoundedRangeIncompleteDynamic - Interface in org.anchoranalysis.core.index.bounded
- boundedVoxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- BoundedVoxels<T> - Class in org.anchoranalysis.image.voxel
-
Voxel-data that is bounded to exist in a particular bounding-box in an image.
- BoundedVoxels(BoundedVoxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels
-
Copy constructor
- BoundedVoxels(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels
-
Creates voxels bounded to match the entire voxel-data at the origin.
- BoundedVoxels(BoundingBox, Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.BoundedVoxels
-
Creates voxels with a corresponding bounding box.
- BoundedVoxelsFactory - Class in org.anchoranalysis.image.voxel
- boundingBox() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- boundingBox() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
A bounding-box that associates voxels to a particular part of an image
- boundingBox() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- boundingBox() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
-
A bounding-box enclosing the voxelized representation of the mark
- boundingBox() - Method in class org.anchoranalysis.spatial.box.BoundedList
-
A bounding-box that must contain all elements in the collection
- BoundingBox - Class in org.anchoranalysis.spatial.box
-
A bounding-box in 2 or 3 dimensions.
- BoundingBox(Extent) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox
-
Constructs a bounding-box to cover the entirety of a certain extent.
- BoundingBox(Point3d, Point3d) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox
-
Creates from two
doublepoints (a minimum corner and a maximum corner). - BoundingBox(ReadableTuple3i, Extent) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox
- BoundingBox(ReadableTuple3i, ReadableTuple3i) - Constructor for class org.anchoranalysis.spatial.box.BoundingBox
-
Creates from two
intpoints (a minimum corner and a maximum corner). - BoundingBoxAlongAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
- BoundingBoxAlongAxisBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
- BoundingBoxCalculator - Class in org.anchoranalysis.mpp.mark.conic
-
Functions to calculate a bounding-box for a point surrounded by some form of radii
- BoundingBoxContains - Class in org.anchoranalysis.spatial.box
-
Does a bounding box contain other objects? e.g.
- BoundingBoxContains(BoundingBox) - Constructor for class org.anchoranalysis.spatial.box.BoundingBoxContains
- BoundingBoxDistance - Class in org.anchoranalysis.spatial.box
-
Calculates distance between two bounding boxes
- BoundingBoxesOnPlane - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
Describes a set of bounding boxes on top of a plane
- BoundingBoxesOnPlane(Extent) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
- BoundingBoxesOnPlane(Extent, BoundingBox) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
- BoundingBoxExtent - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
- BoundingBoxExtent() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
- BoundingBoxExtentAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
- BoundingBoxExtentAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxExtentAlongAxis
- boundingBoxFlattened() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
-
The bounding-box flattened in z dimension
- boundingBoxFor(T) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask
-
A bounding-box for a given element.
- boundingBoxForRegion(VoxelizedMark) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- BoundingBoxFromPoints - Class in org.anchoranalysis.image.core.points
-
Creates a bounding-box from one or more points
- BoundingBoxIntersection - Class in org.anchoranalysis.mpp.feature.addcriteria
- BoundingBoxIntersection - Class in org.anchoranalysis.spatial.box
-
Methods for checking intersection between a particular bounding-box and others
- BoundingBoxIntersection() - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
- BoundingBoxIntersection(BoundingBox) - Constructor for class org.anchoranalysis.spatial.box.BoundingBoxIntersection
- BoundingBoxMaximumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
- BoundingBoxMaximumAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMaximumAlongAxis
- BoundingBoxMerger - Class in org.anchoranalysis.spatial.box
- BoundingBoxMinimumAlongAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
- BoundingBoxMinimumAlongAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMinimumAlongAxis
- BoundingBoxNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
- BoundingBoxNumberVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxNumberVoxels
- boundingBoxThatSpansInput(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
- boundingBoxThatSpansInput(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
- boundingBoxThatSpansInput(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
-
Creates a bounding-box that tightly fits the input to a particular table row (could be for one or more objects)
- BoundingBoxUnion - Class in org.anchoranalysis.spatial.box
-
Performs union of a bounding-box with other entities
- BoundingBoxUnion(BoundingBox) - Constructor for class org.anchoranalysis.spatial.box.BoundingBoxUnion
- BoundingBoxZDistance - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
-
Measures the amount of distance in Z for the bounding box.
- BoundingBoxZDistance() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZDistance
- BoundingBoxZOverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
-
Measures the amount of bounding box overlap in the Z dimension
- BoundingBoxZOverlapRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZOverlapRatio
- BoundMinMax - Class in org.anchoranalysis.mpp.bean.bound
- BoundMinMax() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax
- BoundMinMax(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax
- BoundMinMax(BoundMinMax) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundMinMax
- BoundOutputter<T> - Class in org.anchoranalysis.io.generator.sequence
-
An outputter bound together with
OutputPatternand a generator. - BoundOutputter(OutputterChecked, OutputPattern, Generator<T>) - Constructor for class org.anchoranalysis.io.generator.sequence.BoundOutputter
- BoundPhysicalExtent - Class in org.anchoranalysis.mpp.bean.bound
- BoundPhysicalExtent() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
- BoundPhysicalExtent(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
- BoundPhysicalExtent(BoundPhysicalExtent) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
- BoundReplaceStrategy<T extends FeatureInput,S extends ReplaceStrategy<T>> - Class in org.anchoranalysis.feature.session.strategy.replace.bind
-
Attaches a replacement-strategy to a session lazily (i.e.
- BoundReplaceStrategy(Function<CacheCreator, S>) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.bind.BoundReplaceStrategy
- BoundsFromRange<T> - Class in org.anchoranalysis.core.index.bounded
- BoundsFromRange(GetterFromIndex<T>, BoundedRangeIncomplete) - Constructor for class org.anchoranalysis.core.index.bounded.BoundsFromRange
- BoundUnitless - Class in org.anchoranalysis.mpp.bean.bound
- BoundUnitless() - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless
- BoundUnitless(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless
- BoundUnitless(BoundUnitless) - Constructor for class org.anchoranalysis.mpp.bean.bound.BoundUnitless
- box() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
- box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.Mark
- box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
- box(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
- box(FeatureInputPairMemo, Function<FeatureInputPairMemo, VoxelizedMarkMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
- box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
-
How we create our scaled masks
- box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
- box(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.Overlay
-
A bounding-box around the overlay
- box(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains
-
Is this other bounding-box FULLY contained within this bounding box?
- boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.Mark
- boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.PointList
- boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
- boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
- boxAllRegions(Dimensions) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
- boxCopyTo(BoundingBox, Voxels<T>, BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.Base
- boxCopyTo(BoundingBox, Voxels<T>, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
-
Copies a bounding-box area to another
Voxels - boxFromBounds(Point3d, double, boolean, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.conic.BoundingBoxCalculator
-
Calculates a bounding box for a point with a scalar radius in all dimensions
- boxFromBounds(Point3d, DoubleMatrix1D, boolean, Dimensions) - Static method in class org.anchoranalysis.mpp.mark.conic.BoundingBoxCalculator
-
Calculates a bounding box for a point with varying radii in each dimension (that have already been resolved into a matrix)
- boxIterator() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
- boxList(Dimensions, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- boxList(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- boxList(DrawOverlay, Dimensions) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- BoxPlot<T> - Class in org.anchoranalysis.plot.index
- BoxPlot(String, String[], GetForSeries<T, String>, GetForSeries<T, BoxAndWhiskerItem>, GetForSeries<T, Paint>) - Constructor for class org.anchoranalysis.plot.index.BoxPlot
- BranchChannels - Class in org.anchoranalysis.plugin.io.bean.stack.writer
-
Uses different raster-writers depending on the number/type of channels.
- BranchChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
- BranchIfDebug<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Uses one input-manager normally, but a different one if in debug mode
- BranchIfDebug() - Constructor for class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
- BranchStack - Class in org.anchoranalysis.plugin.io.bean.stack.writer
-
Uses different raster-writers depending on whether it is always 2D (not a z-stack) or possibly 3D.
- BranchStack() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
- bridge(int, H) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
- bridge(int, H) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridgeWithIndex
- bridge(int, H) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridgeWithoutIndex
- Bridge - Class in org.anchoranalysis.plugin.image.bean.object.match
-
Matches to another object, and then uses that object to bridge to another
- Bridge() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Bridge
- bridgeElement(int, S) - Method in interface org.anchoranalysis.core.index.BridgeElementWithIndex
- BridgeElementWithIndex<S,D,E extends Exception> - Interface in org.anchoranalysis.core.index
- buffer() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
-
The associated buffer for storing the voxels.
- buffer(VoxelBuffer<U>, Extent, Function<U, T>, Function<AbstractNativeImg<S, T>, S>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.Wrap
- BufferedImageFactory - Class in org.anchoranalysis.image.core.stack.bufferedimage
- BufferedImageOverlay - Class in org.anchoranalysis.image.core.stack.bufferedimage
- bufferListForSlice(int) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
- bufferRel(int) - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
- bufferValueEqualTo(T, int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
-
Checks if the current value from a buffer is equal to a constant value
- bufferValueGreaterThan(T, int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
-
Checks if the current value from a buffer is greater than a constant value
- bv - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
- byDimension(int) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
- byDimension(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- byDimension(AxisType) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
- byDimension(AxisType) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- bySymbol() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
-
Calculates a feature if only an symbol (ID/name) is known, which refers to another feature.
- bySymbol() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
- ByteRepresentationForChannel - Interface in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
-
Creates or retrieves a byte representation of the voxels for a particular slice.
- bytesForSlice(int) - Method in interface org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.ByteRepresentationForChannel
-
The byte-representation of the voxels for a particular slice.
- bytesPerPixel - Variable in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
- bytesPerPixel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
- bytesPerPixel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
- bytesPerPixel() - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
C
- cache(CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.cache.CachedSupplier
-
Creates a cached-version of a
CheckedSupplier - cache(StoreSupplier<T>) - Static method in interface org.anchoranalysis.core.identifier.provider.store.StoreSupplier
-
Memoizes (caches) the supplied object, and returning it with an identical interface
- cache(CheckedProgressingSupplier<T, E>) - Static method in class org.anchoranalysis.core.progress.CachedProgressingSupplier
-
Creates a cached-version of a
CheckedProgressingSupplier - cache(NamedStacksSupplier) - Static method in interface org.anchoranalysis.image.core.stack.NamedStacksSupplier
- cache(SerializedObjectSupplier<T>) - Static method in interface org.anchoranalysis.io.manifest.finder.SerializedObjectSupplier
- CACHE_NAME_FIRST - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
- CACHE_NAME_MERGED - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
- CACHE_NAME_SECOND - Static variable in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
- CacheAndReuseStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.strategy.replace
-
Reuse (without needing to invalidate) an existing session-input as stored in a least-recently used cache, otherwise create a new one.
- CacheAndReuseStrategy(CacheCreator) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.CacheAndReuseStrategy
- CacheCreator - Interface in org.anchoranalysis.feature.calculate.cache
- CacheCreatorSimple - Class in org.anchoranalysis.feature.session.cache.creator
- CacheCreatorSimple(FeatureList<? extends FeatureInput>, SharedFeatureMulti, FeatureInitParams, Logger) - Constructor for class org.anchoranalysis.feature.session.cache.creator.CacheCreatorSimple
- CachedProgressingSupplier<T,E extends Exception> - Class in org.anchoranalysis.core.progress
-
Memoizes (caches) a call to
CheckedProgressingSupplier - CachedSupplier<T,E extends Exception> - Class in org.anchoranalysis.core.cache
-
Memoizes (caches) a
CheckedSupplier - CachedSupplierBase<T> - Class in org.anchoranalysis.core.cache
-
Base class for functions that memoize (cache) a call to an interface
- CachedSupplierBase() - Constructor for class org.anchoranalysis.core.cache.CachedSupplierBase
- cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
- cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
- cacheName() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
- cacheResettable(StoreSupplier<T>) - Static method in interface org.anchoranalysis.core.identifier.provider.store.StoreSupplier
-
Memoizes (caches) the supplied object, and returning it with a
CachedSupplierinterface - cachesToAvoidInvalidating() - Method in class org.anchoranalysis.feature.session.strategy.child.CheckCacheForSpecificChildren
- cachesToAvoidInvalidating() - Method in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
- cachesToAvoidInvalidating() - Method in interface org.anchoranalysis.feature.session.strategy.child.FindChildStrategy
-
If set, these particular-caches are exceptionall NOT invalidated during the typical invalidation operation on their parent.
- CacheSupplier<T extends FeatureInput,E extends Exception> - Interface in org.anchoranalysis.feature.session.strategy.child
- CacheTransferSource<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.strategy.child
-
An existing cache that can be used as a source for child-caches elsewhere
- CacheTransferSource(CacheSupplier<T, OperationFailedException>, Set<ChildCacheName>) - Constructor for class org.anchoranalysis.feature.session.strategy.child.CacheTransferSource
- CacheTransferSourceCollection - Class in org.anchoranalysis.feature.session.strategy.child
- CacheTransferSourceCollection() - Constructor for class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
- calc(double, double, double, boolean, boolean) - Static method in class org.anchoranalysis.plugin.operator.feature.score.GaussianScoreCalculator
- calc(FeatureList<T>, SessionInput<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCalculator
-
Calculates a feature-list throwing an exception if there is an error
- calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
- calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
- calc(CalculateForChild<T>, Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
- calc(SessionInput<T>, FeatureCalculation<U, T>, Function<ResolvedCalculation<U, T>, CalculateInputFromDelegateOption<S, T, U>>, Feature<S>, ChildCacheName, double) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
-
Calculates a feature using a cached-calculation as delegate, and optional Params return value
- calc(FeatureInputObjectCollection) - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
- calc(FeatureInputObjectCollection) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.collection.NumberObjects
- calc(FeatureInputSingleObject, Ellipsoid) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.AxisRatioEllipsoid
- calc(FeatureInputSingleObject, Ellipsoid) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
- calc(FeatureInputSingleObject, Ellipsoid) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.Ellipsoidicity
- calc(ObjectMask) - Method in interface org.anchoranalysis.image.feature.evaluator.PayloadCalculator
- calc(ObjectMask, boolean) - Static method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
- calc(FeatureInputMarkCollection) - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureMarkCollection
- calc(FeatureInputMarkCollection) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.collection.NumberMarks
- calc(MemoCollection, EnergySchemeWithSharedFeatures, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
- calculate(int[]) - Method in class org.anchoranalysis.image.feature.bean.score.VoxelScore
- calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
- calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
- calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
- calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
- calculate(int[]) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
- calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.image.bean.spatial.ScaleCalculator
- calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorConstant
- calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorInverted
- calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorMinXYRes
- calculate(Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
- calculate(Feature<S>, FeatureCalculation<S, T>, ChildCacheName) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild
-
Calculates a feature in a child-cache using a new input created from a
FeatureCalculation - calculate(Feature<S>, S, ChildCacheName) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild
-
Calculates a feature in a child-cache
- calculate(Feature<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
-
Calculates the result of a feature using this input
- calculate(Feature<T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
- calculate(Feature<T>, SessionInput<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCalculator
-
Calculate a feature with particular values
- calculate(FeatureList<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
-
Calculates the results of several features using this input
- calculate(FeatureList<T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
- calculate(ChildCacheName, S, Function<CalculationResolver<S>, ResolvedCalculation<U, S>>) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculateForChild
-
Calculates a
FeatureCalculationin a child-cache - calculate(ResolvedCalculation<S, T>) - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
-
Calculates a resolved Feature-calculation
- calculate(ResolvedCalculation<S, T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
- calculate(SessionInput<FeatureInput>) - Method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculation
- calculate(SessionInput<FeatureInputResults>) - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
- calculate(SessionInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
- calculate(SessionInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
- calculate(SessionInput<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
- calculate(SessionInput<FeatureInputObjectCollection>) - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.First
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Merged
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Minimum
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.RatioFirstToSecond
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.Second
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.SubtractSecondFromFirst
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
- calculate(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxNumberVoxels
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMagnitude
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityCenterSlice
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityMIP
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberContourVoxelsOnSlice
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberVoxelsOnSlice
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
- calculate(SessionInput<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.Ellipticity
- calculate(SessionInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
- calculate(SessionInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
- calculate(SessionInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
- calculate(SessionInput<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
- calculate(SessionInput<FeatureInputMarkCollection>) - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureMarkCollection
- calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureMark
- calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
- calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.FeatureMarkEccentricity
- calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.MaxRatioRadii
- calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.OrderedRadius
- calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
- calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
- calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.MarkEllipseCircumEstimate
- calculate(SessionInput<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.Volume
- calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.AsCollection
- calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.AsSingleMark
- calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CoefficientOfVarianceFromAll
- calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MeanFromAll
- calculate(SessionInput<FeatureInputAllMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.NumberMarks
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZDistance
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZOverlapRatio
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.MinimumDistanceByDimension
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeatureAsIndividualProportionate
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.MinFeatureAsIndividual
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapNumVoxels
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapNumVoxelsMask
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatio
- calculate(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatioMask
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsMark
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.BBoxRatio
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MaxSliceArea
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Size
- calculate(SessionInput<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.Feature
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Constant
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Reference
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.operator.Sum
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.DataTypeMaxIntensity
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AbsoluteValue
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Multiply
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.Maximum
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.Mean
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.MeanGeometric
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.Minimum
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.NormalizedRange
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
- calculate(SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
- calculate(FeatureCalculation<S, T>) - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
-
Calculates a feature-calculation after resolving it against the main cache
- calculate(FeatureCalculation<S, T>) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
- calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.Count
- calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
- calculate(FeatureInputResults) - Method in class org.anchoranalysis.feature.bean.results.StatisticForFeature
- calculate(FeatureInputPairObjects) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
- calculate(FeatureInputPairObjects, FeatureList<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
- calculate(FeatureInputSingleObject) - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
- calculate(FeatureInputSingleObject, FeatureList<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
- calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
- calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedSingle
- calculate(T) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti
-
Performs one calculation throwing an exception if something goes wrong
- calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
- calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
- calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
- calculate(T) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingle
-
Performs one calculation throwing an exception if something goes wrong
- calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleChangeInput
- calculate(T) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleFromMulti
- calculate(T) - Method in class org.anchoranalysis.feature.session.SequentialSession
-
Calculates one params for each feature.
- calculate(T, ErrorReporter, boolean) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti
-
Performs one calculation, either calling
FeatureCalculatorMulti.calculate(T)orFeatureCalculatorMulti.calculateSuppressErrors(T, org.anchoranalysis.core.log.error.ErrorReporter)depending on a flag - calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
- calculate(T, FeatureList<T>) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti
-
Performs one calculation on a sub-set of the feature list throwing an exception if something goes wrong
- calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
- calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
- calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
- calculate(T, FeatureList<T>) - Method in class org.anchoranalysis.feature.session.SequentialSession
- calculateAcceptanceProb(Kernel<?>, Optional<T>, T, int, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.AccptProbCalculator
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
- calculateAcceptanceProbability(int, int, double, Dimensions, double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
- calculateBound(Point3d, RotationMatrix) - Method in class org.anchoranalysis.mpp.bean.bound.BoundCalculator
- calculateBound(Point3d, RotationMatrix) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
- calculateBound(Point3d, RotationMatrix) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
- calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
- calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
- calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
- calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleaving
- calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
- calculateBytesPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
- calculateCheckInitialized(SessionInput<T>) - Method in class org.anchoranalysis.feature.bean.Feature
- calculateConnectedComponentID(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- calculateContext(MarkFactoryContext) - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
- calculateCornerMax() - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
The maximum (right-most) point inside the box.
- calculateCornerMaxExclusive() - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
The maximum (right-most) point just outside the box.
- calculateCountNonZero() - Method in class org.anchoranalysis.math.histogram.Histogram
- calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
- calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToFirst
- calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMaxVolume
- calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMerged
- calculateDenominator(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToSecond
- calculateDensityRatio(double, double, int) - Method in class org.anchoranalysis.mpp.bean.anneal.AnnealScheme
- CalculateDeriveMarkCollectionInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
- CalculateDeriveMarkCollectionInput() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
- CalculateDeriveMarkInput - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
- CalculateDeriveMarkInput() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
- CalculateDeriveObjectInput - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
- CalculateDeriveObjectInput(int) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
- CalculateDeriveSingleMemoFromPair - Class in org.anchoranalysis.mpp.feature.bean.energy.element
- CalculateDeriveSingleMemoFromPair(boolean) - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
- CalculateDilation - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
- CalculateDilationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
- CalculateDilationMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
- CalculateDilationMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
- calculateEccentricity(double, double) - Static method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
- CalculateEllipseLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipse
- CalculateEllipseLeastSquares() - Constructor for class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
- CalculateEllipsoidLeastSquares - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid
- CalculateErosion - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
- CalculateErosionMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
- CalculateErosionMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
- CalculateErosionMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
- calculateFeatureByIdentifier(String, SessionInput<T>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSymbolCalculator
-
Searches for a feature that matches a particular identifier
- calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputObjectCollection>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectCollection
- calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<FeatureInputSingleObject>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObject
- calculateFeatureOn(ObjectCollection, FeatureCalculatorSingle<T>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
- calculateFeaturesForObjects(ObjectCollection, EnergyStack, CalculateFeaturesForObjects.LabelsForInput<T>) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects
- CalculateFeaturesForObjects<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.feature.calculator
- CalculateFeaturesForObjects(CombineObjectsForFeatures<T>, InitParamsWithEnergyStack, boolean, InputProcessContext<FeatureTableCalculator<T>>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects
- CalculateFeaturesForObjects.LabelsForInput<T extends FeatureInput> - Interface in org.anchoranalysis.plugin.image.task.feature.calculator
- calculateForAxis(Dimensions, AxisType) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Extent
- calculateForAxis(Dimensions, AxisType) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
- calculateForAxis(Dimensions, AxisType) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize
- calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
- calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
- calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
- calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
- calculateForChannel(SessionInput<FeatureInputSingleObject>, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
- CalculateForChild<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
-
Performs calculations using child-caches instead of the main cache
- calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.DotProductOrientationToVector
- calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.EllipsoidAxisRatio
- calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.EllipsoidMaxAreaIntersectingPlane
- calculateForEllipsoid(Ellipsoid, Orientation, RotationMatrix, Vector3d) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
- calculateForNewMark(VoxelizedMarksWithEnergy, Set<Mark>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
- calculateForNewMark(MarksFromPartition, Set<Mark>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
- calculateForNewMark(T, Set<Mark>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
- calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShell
- calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
- calculateForShell(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellMaxSlice
- calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
- calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
- calculateForVoxel(int, int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
- calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
- calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
- calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
- calculateFromAllMoments(ImageMoments) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
- calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Area
- calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
- calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
- calculateFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.Volume
- calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
- calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
- calculateFromSpecificMoment(EigenvalueAndVector) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
-
Calculates the result for the specific moment identified by index
- CalculateHistogram - Class in org.anchoranalysis.plugin.image.feature.stack.calculation
- CalculateHistogram(int) - Constructor for class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
- CalculateHistogramMasked - Class in org.anchoranalysis.plugin.image.feature.stack.calculation
-
Calculated a histogram for a specific region on a channel, as identified by a mask in another channel
- CalculateHistogramMasked(int, int) - Constructor for class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
- CalculateIncrementalOperationMap - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
- CalculateIncrementalOperationMap(boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
- CalculateIncrementalOperationMap(CalculateIncrementalOperationMap) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
- CalculateInputFromDelegate<S,T extends FeatureInput,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate
-
A base class for Cached-Calculations that generate a Params for feature-calculation using an existing "delegate" calculation
- CalculateInputFromDelegate(ResolvedCalculation<U, T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
- CalculateInputFromDelegate(FeatureCalculation<U, T>, CalculationResolver<T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
- CalculateInputFromDelegateOption<S extends FeatureInput,T extends FeatureInput,U> - Class in org.anchoranalysis.plugin.image.feature.object.calculation.delegate
-
Like
CalculateInputFromDelegateexcept assumes optional return value and no parameters - CalculateInputFromDelegateOption(ResolvedCalculation<U, T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
-
The constructor
- CalculateInputFromPair - Class in org.anchoranalysis.image.feature.object.calculation
-
Calculates a single-input from a pair
- CalculateInputFromPair(CalculateInputFromPair.Extract) - Constructor for class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
- CalculateInputFromPair.Extract - Enum in org.anchoranalysis.image.feature.object.calculation
- CalculateIntersecting - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
- CalculateIntersecting(ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>, int) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
- calculateLevel(Histogram) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel
-
Determines a voxel intensity that can be used for thresholding.
- calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
- calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
- calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
- calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
- calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
- calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
- calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
- calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
- calculateLevel(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
- CalculateLevel - Class in org.anchoranalysis.image.bean.threshold
-
Calculates a threshold-level from a histogram.
- CalculateLevel - Class in org.anchoranalysis.plugin.image.feature.bean.score
- CalculateLevel() - Constructor for class org.anchoranalysis.image.bean.threshold.CalculateLevel
- CalculateLevel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
- CalculateLevelBase - Class in org.anchoranalysis.plugin.image.feature.bean.score
- CalculateLevelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
- calculateLevelIncoming(Histogram) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
- CalculateLevelListBase - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
- CalculateLevelListBase() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
- CalculateLevelOne - Class in org.anchoranalysis.image.bean.threshold
- CalculateLevelOne() - Constructor for class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
- CalculateLevelRelativeToThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
- CalculateLevelRelativeToThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
- calculateMaximum() - Method in class org.anchoranalysis.math.histogram.Histogram
-
Calculates the maximum of the histogram values i.e.
- calculateMaybeSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
- calculateMeanIntensityObject(Channel, ObjectMask) - Static method in class org.anchoranalysis.plugin.image.intensity.IntensityMeanCalculator
- calculateMeanIntensityObject(Channel, ObjectMask, boolean) - Static method in class org.anchoranalysis.plugin.image.intensity.IntensityMeanCalculator
- calculateMemoryUsage() - Static method in class org.anchoranalysis.core.system.MemoryUtilities
- calculateMinimum() - Method in class org.anchoranalysis.math.histogram.Histogram
-
Calculates the minimum of the histogram values i.e.
- calculateMinMax(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds
- calculateMode() - Method in class org.anchoranalysis.math.histogram.Histogram
- calculateMode(int) - Method in class org.anchoranalysis.math.histogram.Histogram
-
Calculates the mode of the histogram values i.e.
- calculateNewMaxCurrentValue() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
- CalculateNumVoxels - Class in org.anchoranalysis.image.feature.object.calculation
- CalculateNumVoxels(boolean) - Constructor for class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
- CalculateObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
- CalculateObjectMask(int, ResolvedCalculationMap<ObjectMask, FeatureInputSingleObject, Integer>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
- CalculateObjectMask(CalculateObjectMask) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
-
Copy constructor
- CalculateOverlap - Class in org.anchoranalysis.plugin.mpp.feature.overlap
- CalculateOverlap(int) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
- CalculateOverlapMask - Class in org.anchoranalysis.plugin.mpp.feature.overlap
- CalculateOverlapMask(int, int, byte) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
- CalculateOverlapMIP - Class in org.anchoranalysis.plugin.mpp.feature.overlap
- CalculateOverlapMIP(int) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
- CalculateOverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.overlap
- CalculateOverlapMIPBase(int) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
- CalculateOverlapMIPRatio - Class in org.anchoranalysis.plugin.mpp.feature.overlap
- CalculateOverlapMIPRatio(int) - Constructor for class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
- calculateOverlapRatio(ObjectMask, ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.OverlapCalculator
- calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
- calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
- calculateOverlapResult(double, MaxIntensityProjectionPair) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
- calculatePath() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
- calculatePath() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
- calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
- calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.PointsFromOrientationProposer
- calculatePoints(Point3d, Orientation, boolean, RandomNumberGenerator, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
- CalculatePointsFromOutline - Class in org.anchoranalysis.plugin.points.calculate
- CalculatePointsFromOutline() - Constructor for class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
- calculateResultsForInput(ProvidesStackInput, InputProcessContext<FeatureList<FeatureInputStack>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
- calculateResultsForInput(FileInput, InputProcessContext<FeatureList<FeatureInputHistogram>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
- calculateResultsForInput(T, InputProcessContext<FeatureList<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
- calculateRunningSum(Mask, Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.core.mask.IterateVoxelsMask
-
Calculates the sum and count across voxels intensity that correspond to on voxels on a mask
- CalculateShellObjectMask - Class in org.anchoranalysis.plugin.image.feature.object.calculation.single
- CalculateShellObjectMask(ResolvedCalculation<ObjectMask, FeatureInputSingleObject>, ResolvedCalculation<ObjectMask, FeatureInputSingleObject>, int, boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
- calculateSigma(Dimensions, MessageLogger) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.image.feature.histogram.Mean
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.CoefficientOfVariation
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Kurtosis
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Max
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Median
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Min
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Mode
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.NumberDistinctValues
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Skewness
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.StdDev
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Sum
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.TotalCount
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Variance
- calculateStatisticFrom(Histogram) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
- calculateSum() - Method in class org.anchoranalysis.math.histogram.Histogram
- calculateSumCubes() - Method in class org.anchoranalysis.math.histogram.Histogram
- calculateSumSquares() - Method in class org.anchoranalysis.math.histogram.Histogram
- calculateSuppressErrors(FeatureInputPairObjects, ErrorReporter) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
- calculateSuppressErrors(FeatureInputSingleObject, ErrorReporter) - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
- calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
- calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedSingle
- calculateSuppressErrors(T, ErrorReporter) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti
-
Performs one calculation recording the error to an ErrorReporter if anything goes wrong, but throwing no exception
- calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
- calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
- calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
- calculateSuppressErrors(T, ErrorReporter) - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingle
-
Performs one calculation recording the error to an ErrorReporter if anything goes wrong, but throwing no exception
- calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleChangeInput
- calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleFromMulti
- calculateSuppressErrors(T, ErrorReporter) - Method in class org.anchoranalysis.feature.session.SequentialSession
-
Calculates the next-object in our sequential series, reporting any exceptions into a reporter log
- calculateTemperature(int) - Method in class org.anchoranalysis.mpp.bean.anneal.AnnealScheme
- calculateTemperature(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
- calculateTemperature(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.NoAnnealing
- calculateVolume() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- calculateVolume() - Method in class org.anchoranalysis.spatial.Extent
- calculateVolumeAsInt() - Method in class org.anchoranalysis.spatial.Extent
- calculateWith(Feature<T>, T, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
-
Starts a feature-session for a single feature - and performs a calculation
- calculateWithChannel(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
- calculateWithChannel(ObjectMask, Channel) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.HasTouchingVoxels
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumTouchingVoxelFaces
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumTouchingVoxels
- calculateWithIntersection(ObjectMask, ObjectMask, BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
- calculateWithParameters(ObjectMask, OutlineKernelParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder
- calculateWithParameters(ObjectMask, OutlineKernelParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
- calculateWithParameters(ObjectMask, OutlineKernelParameters, CheckedSupplier<EnergyStack, FeatureCalculationException>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
- calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
- calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
- calculateWithResolution(double, Resolution) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
- calculateZScore(double, double, double) - Static method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
- CalculationResolver<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
-
Searches a cache to reuses a
FeatureCalculationif it already exists. - calculator() - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache
-
A means of calculating feature values using this cache.
- calculator() - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
- calculator() - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
- calculatorForAll(FeatureList<T>) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider
-
Calculates all image-features in the feature-store
- calculatorSingleFromProvider(FeatureListProvider<T>, String) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider
-
Calculates a single-feature that comes from a provider (but can reference the other features from the store)
- call() - Method in class org.anchoranalysis.experiment.task.processor.CallableJob
- call(CheckedSupplier<T, E>) - Method in class org.anchoranalysis.core.cache.CachedSupplierBase
- CallableJob<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.task.processor
-
A job derived from a
Taskthat can be placed on different threads - CallableJob(Task<T, S>, ParametersUnbound<T, S>, JobState, JobDescription, ConcurrentJobMonitor, Optional<MessageLogger>, int) - Constructor for class org.anchoranalysis.experiment.task.processor.CallableJob
-
Constructor
- callChannelIfSupported(int, BiConsumer<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>>, Consumer<Channel>) - Method in class org.anchoranalysis.image.core.stack.ChannelMapper
- callEachPointInNeighborhood(Point3i, Neighborhood, boolean, ProcessVoxelNeighbor<T>, int, int) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.IterateVoxelsNeighbors
-
Iterate over each point in the neighborhood of an existing point.
- canEqual(Object) - Method in class org.anchoranalysis.bean.shared.path.RootPath
- canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
- canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
- canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
- canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
- canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
- canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
- canEqual(Object) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- canEqual(Object) - Method in class org.anchoranalysis.core.concurrency.WithPriority
- canEqual(Object) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
- canEqual(Object) - Method in class org.anchoranalysis.core.index.Indexable
- canEqual(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
- canEqual(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
- canEqual(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputNull
- canEqual(Object) - Method in class org.anchoranalysis.feature.io.name.SimpleName
- canEqual(Object) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
- canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
- canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
- canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
- canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
- canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
- canEqual(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
- canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
- canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
- canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
- canEqual(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
- canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
- canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
- canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
- canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
- canEqual(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
- canEqual(Object) - Method in class org.anchoranalysis.image.feature.stack.FeatureInputStack
- canEqual(Object) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
- canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
- canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- canEqual(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
- canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
- canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
- canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
- canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
- canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
- canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
- canEqual(Object) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
- canEqual(Object) - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
- canEqual(Object) - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
- canEqual(Object) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
- canEqual(Object) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- canEqual(Object) - Method in class org.anchoranalysis.overlay.IndexableOverlays
- canEqual(Object) - Method in class org.anchoranalysis.plot.AxisLimits
- canEqual(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- canEqual(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
- canEqual(Object) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
- canEqual(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
- canEqual(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Specific
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
- canEqual(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
- canEqual(Object) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
- canEqual(Object) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- canEqual(Object) - Method in class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
- canEqual(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
- canEqual(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
- canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Point3d
- canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Point3f
- canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Point3i
- canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3f
- canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- canEqual(Object) - Method in class org.anchoranalysis.spatial.point.Vector3d
- canExceptionBeCombined(Throwable) - Method in exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
- canExceptionBeCombined(Throwable) - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
- canExceptionBeCombined(Throwable) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
- canExceptionBeCombined(Throwable) - Method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
- canExceptionBeSkipped(Throwable) - Method in exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
- canExceptionBeSkipped(Throwable) - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
- canExceptionBeSkipped(Throwable) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
- canExceptionBeSkipped(Throwable) - Method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
- capacity() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
-
The capacity of the buffer ala
Buffer.capacity. - capacity() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
-
The capacity (i.e.
- castTo() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
-
Casts voxels to a particular type
- Cell - Class in org.anchoranalysis.image.bean.spatial.arrange
- Cell() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Cell
- centerOfGravity() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Calculates center-of-gravity across all axes
- centerOfGravity() - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
Similar to
BoundingBox.midpoint()but not always identical. - centerOfGravity(AxisType) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Calculates center-of-gravity for one specific axis only
- CenterOfGravity - Class in org.anchoranalysis.image.feature.bean.object.single
- CenterOfGravity() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
- CenterOfGravity(AxisType) - Constructor for class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
-
Creates for a specific axis.
- CenterOnMask - Class in org.anchoranalysis.plugin.mpp.bean.check
- CenterOnMask() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.CenterOnMask
- centerPoint() - Method in class org.anchoranalysis.mpp.mark.Mark
- centerPoint() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
- centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.PointList
- centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
- centerPoint() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
- centerPoint() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
- CenterSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
- CenterSlice() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
- CenterSliceBase - Class in org.anchoranalysis.plugin.mpp.bean.region
- CenterSliceBase() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
- CenterSliceWindow - Class in org.anchoranalysis.plugin.mpp.bean.region
-
Like {#link org.anchoranalysis.plugin.mpp.bean.region.CenterSlice} but considers more than one slice, specifically centerSlice+- windowSize
- CenterSliceWindow() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
- chainCode(int, int, int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
- chainCodes(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
-
Decodes a chain-code into a point
- ChainCodesDirection - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
-
Maps directions to chain codes
- CHANGE_EXISTING_CHANNEL - org.anchoranalysis.image.core.channel.convert.ConversionPolicy
- ChangeableOutputSequence<T,S> - Class in org.anchoranalysis.plugin.image.task.bean.format
- ChangeableOutputSequence() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
- changedMarkIDArray() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
-
The mark ids that were changed in the last energy calculation for the kernel
- changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
- changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
- changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
- changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
- changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
- changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
- changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
- changedMarkIDArray() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
- changedOffset(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
- changeExtent(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
- changeExtentZ(int) - Method in class org.anchoranalysis.spatial.box.BoundingBox
- changeInput(U) - Method in class org.anchoranalysis.experiment.task.InputBound
-
Immutably changes the input-object
- changeIntensity(Voxels<?>, IntUnaryOperator) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
-
Changes each voxel, reading and writing the buffer as an
int. - changePrefix(DirectoryWithPrefix) - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
-
Creates a new
OutputterTargetwith a changed prefix. - changePrefix(DirectoryWithPrefix, Optional<WriteOperationRecorder>) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
-
Creates a
OutputterCheckedwith a changed prefix andWriteOperationRecorder. - changeZ(int, int) - Method in class org.anchoranalysis.spatial.box.BoundingBox
- channel() - Method in class org.anchoranalysis.image.core.mask.Mask
-
The underlying channel which contains the binary-values.
- channel(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
- Channel - Class in org.anchoranalysis.image.core.channel
-
A channel from an image.
- Channel(Voxels<?>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.core.channel.Channel
-
Constructor
- channelAt(int) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- ChannelConverter<T> - Class in org.anchoranalysis.image.core.channel.convert
-
Converts a channel from one type to another specific type.
- ChannelConverter(VoxelDataType, VoxelsConverter<T>, VoxelsFactoryTypeBound<T>) - Constructor for class org.anchoranalysis.image.core.channel.convert.ChannelConverter
- ChannelConverterAttached<S,T> - Interface in org.anchoranalysis.image.core.channel.convert.attached
-
A channel-converter that has been permanently attached to a particular object.
- ChannelConverterMulti - Class in org.anchoranalysis.image.core.channel.convert
-
Converts a channel from one type to multiple other types.
- ChannelConverterMulti() - Constructor for class org.anchoranalysis.image.core.channel.convert.ChannelConverterMulti
- ChannelConvertStyle - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Converts a channel(s) at a particular timepoint into a stack(s).
- ChannelConvertStyle() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ChannelConvertStyle
- ChannelFactory - Class in org.anchoranalysis.image.core.channel.factory
-
Creates a channel for one of several data-types
- ChannelFactoryByte - Class in org.anchoranalysis.image.core.channel.factory
- ChannelFactoryByte() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryByte
- ChannelFactoryFloat - Class in org.anchoranalysis.image.core.channel.factory
- ChannelFactoryFloat() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryFloat
- ChannelFactoryInt - Class in org.anchoranalysis.image.core.channel.factory
- ChannelFactoryInt() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryInt
- ChannelFactoryShort - Class in org.anchoranalysis.image.core.channel.factory
- ChannelFactoryShort() - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactoryShort
- ChannelFactorySingleType - Class in org.anchoranalysis.image.core.channel.factory
-
Creates a channel for a specific data-type
- ChannelFactorySingleType(VoxelDataType, VoxelsFactoryTypeBound<?>) - Constructor for class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
- ChannelGetterForTimepoint - Class in org.anchoranalysis.plugin.image.task.channel
- ChannelGetterForTimepoint(ChannelGetter, int) - Constructor for class org.anchoranalysis.plugin.image.task.channel.ChannelGetterForTimepoint
- ChannelMapper - Class in org.anchoranalysis.image.core.stack
-
Helps a retrieve channel and an associated converter and apply operation on them jointly
- ChannelMapper(IntFunction<Channel>, IntFunction<Optional<ChannelConverterAttached<Channel, UnsignedByteBuffer>>>) - Constructor for class org.anchoranalysis.image.core.stack.ChannelMapper
- channelNames() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
- channelNames() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
- ChannelProvider - Class in org.anchoranalysis.image.bean.provider
- ChannelProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProvider
- ChannelProviderBinary - Class in org.anchoranalysis.image.bean.provider
-
A channel-provider based-on two input channel-providers that must be of the same dimensionality
- ChannelProviderBinary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
- ChannelProviderTernary - Class in org.anchoranalysis.image.bean.provider
- ChannelProviderTernary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
- ChannelProviderUnary - Class in org.anchoranalysis.image.bean.provider
- ChannelProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
- channels() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- ChannelSource - Class in org.anchoranalysis.plugin.image.task.grouped
-
Source of channels for aggregating.
- ChannelSource(NamedStacks, ConsistentChannelChecker, Optional<SizeXY>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
- channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
- channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceChannelsPerByteArray
- channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
- channelsPerByteArray(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
- check(Channel, String, Dimensions) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker
-
Checks a channel to make sure it's the same size as an an existing channel
- check(Channel, Mask) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker
- check(Mask, String, Dimensions) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker
-
Checks a channel to make sure it's the same size as an an existing channel
- check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.mpp.feature.bean.mark.CheckMark
-
Checks a mark
- check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
- check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AnySliceCenterOnMask
- check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CenterOnMask
- check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.EllipseBoundsCheck
- check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.Not
- check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
- check(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
- check(T) - Static method in class org.anchoranalysis.test.experiment.BeanTestChecker
-
Checks if a bean has all necessary items, throwing a run-time exception if it does not.
- Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
- Check - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
- Check() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
- Check() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
- checkAndInit(T, P, Logger) - Static method in class org.anchoranalysis.test.experiment.BeanTestChecker
-
Checks if a bean has all necessary items as with
BeanTestChecker.check(T)and also initializes the bean. - CheckCacheForSpecificChildren - Class in org.anchoranalysis.feature.session.strategy.child
-
For particular child-caches, check if a session-input is available from another LRU-cache and reuse.
- CheckCacheForSpecificChildren(Class<?>, CacheTransferSourceCollection) - Constructor for class org.anchoranalysis.feature.session.strategy.child.CheckCacheForSpecificChildren
- checkChannelType(VoxelDataType) - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelChecker
-
Checks that a channel has the same type (max value) as the others
- checkCompatibleWith(Mark) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- CheckedBiConsumer<S,T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
BiConsumerbut can also throw a checked exception. - CheckedBiFunction<S,T,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
BiFunctionbut can also throw a checked exception. - CheckedBooleanSupplier<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
BooleanSupplierbut can also throw an exception. - CheckedConsumer<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Consumes a value and throws an exception
- CheckedFunction<S,V,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
Functionbut can also thrown an exception. - CheckedIntConsumer<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Consumes an
intand throws an exception - CheckedIntFunction<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
IntFunctionbut can also thrown an exception. - CheckedPredicate<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
Predicatebut can also throw an exception. - CheckedProgressingSupplier<R,E extends Exception> - Interface in org.anchoranalysis.core.progress
-
Like
CheckedSupplierbut can update a progress-reporter as the operation progresses. - CheckedRunnable<E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
- CheckedStream - Class in org.anchoranalysis.core.functional
-
Map operations for streams that can throw checked-exceptions
- CheckedStream.ConvertedToRuntimeException - Exception in org.anchoranalysis.core.functional
-
An exception that wraps another exception, but exposes itself as a RuntimeException
- CheckedSupplier<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
Supplierbut can also throw an exception. - CheckedToDoubleBiFunction<T,U,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
ToDoubleBiFunctionbut can also thrown an exception. - CheckedToIntFunction<S,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like
ToIntFunctionbut can also thrown an exception. - CheckedUnaryOperator<T,E extends Exception> - Interface in org.anchoranalysis.core.functional.checked
-
Like a
UnaryOperatorbut allows an exception to be thrown - CheckException - Exception in org.anchoranalysis.mpp.feature.error
- CheckException(String) - Constructor for exception org.anchoranalysis.mpp.feature.error.CheckException
- CheckException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.feature.error.CheckException
- CheckException(Throwable) - Constructor for exception org.anchoranalysis.mpp.feature.error.CheckException
- checkExtentMatch(BoundingBox, BoundingBox) - Static method in class org.anchoranalysis.image.voxel.ExtentMatchHelper
- CheckIfAllowed - Class in org.anchoranalysis.io.output.writer
-
Only allows outputs, if the output-name is allowed in the
OutputterChecked. - CheckIfAllowed(SingleLevelOutputEnabled, Optional<WriterExecuteBeforeEveryOperation>, Writer) - Constructor for class org.anchoranalysis.io.output.writer.CheckIfAllowed
- checkIfConnected() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Determines if an object-mask is connected.
- CheckMark - Class in org.anchoranalysis.mpp.feature.bean.mark
-
A predicate on a mark to check if a condition has been satisfied.
- CheckMark() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.CheckMark
- CheckMarkWithMask - Class in org.anchoranalysis.plugin.mpp.bean.check
- CheckMarkWithMask() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.bean.AnchorBean
-
Checks that a bean's properties conform to expectations.
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
- checkMisconfigured(BeanInstanceMap) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
- checkMisconfigured(BeanInstanceMap) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- CheckMisconfigured - Class in org.anchoranalysis.bean.initializable
-
Routines for checking that particular patterns exist with bean-properties
- CheckParsedFilePathBag - Class in org.anchoranalysis.plugin.io.bean.groupfiles.check
- CheckParsedFilePathBag() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.check.CheckParsedFilePathBag
- checkResultVector(ResultsVector) - Static method in class org.anchoranalysis.test.feature.ConstantsInListFixture
-
checks that a result-vector has the results we expect from the feature-list associated with this fixture
- checkSize(Extent) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
- checkUnsupported3D(Channel) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
- checkUnsupportedObjectMask(Optional<ObjectMask>) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
- checkUnsupportedSeeds(Optional<SeedCollection>) - Static method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
- childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache
-
Gets/creates a child-cache for a given name
- childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
- childCacheFor(ChildCacheName, Class<? extends FeatureInput>, CacheCreator) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
- childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in class org.anchoranalysis.feature.session.strategy.child.CheckCacheForSpecificChildren
- childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
- childCacheFor(FeatureSessionCache<?>, CacheCreator, ChildCacheName, V) - Method in interface org.anchoranalysis.feature.session.strategy.child.FindChildStrategy
-
Selects a child-cache given a parent and a child-name
- ChildCacheName - Class in org.anchoranalysis.feature.calculate.cache
-
A unique identifier for a child-cache name, that uses a class and optionally additionally a part-name a class: guaranteed to be unique for the class an optional part-name (string): a further division of the class into different caches
- ChildCacheName(Class<?>) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName
-
Uses only the class as an identifier - and a blank part-name
- ChildCacheName(Class<?>, int) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName
-
Uses only the class as an identifier - and a integer part-name
- ChildCacheName(Class<?>, String) - Constructor for class org.anchoranalysis.feature.calculate.cache.ChildCacheName
-
Uses both the class and a part-name as an identifier
- children() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- ChooseOneList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
- ChooseOneList() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ChooseOneList
- Circle - Class in org.anchoranalysis.mpp.mark.conic
-
A circle
- Circle() - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle
- Circle(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle
-
Creates with a radius within particular bounds.
- Circle(Circle) - Constructor for class org.anchoranalysis.mpp.mark.conic.Circle
-
Copy constructor
- circleAt(Point2i, double) - Static method in class org.anchoranalysis.test.feature.plugins.objects.CircleObjectFixture
- CircleObjectFixture - Class in org.anchoranalysis.test.feature.plugins.objects
- circumference(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- classificationString(boolean) - Static method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
- classInCurrentJar() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
-
a class which we use to determine the base location for pathRelativeProperties
- clean() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- clean() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
- cleanUp() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
- cleanUp(VoxelPartitionFactory<Histogram>) - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
- cleanUp(VoxelPartitionFactory<T>) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
- cleanUp(VoxelPartitionFactory<T>) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
- cleanUp(VoxelPartitionFactory<T>) - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
- clear() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- clear() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
- clear() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
-
Clears the buffer ala
Buffer.clear(). - clear() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- clear() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- clearBest() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
- clearVisualizationState() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
- clearVisualizationState() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.PointsFromOrientationProposer
- clearVisualizationState() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
- clip(Point3d, Dimensions) - Static method in class org.anchoranalysis.mpp.points.PointClipper
- clip(Point3i, Dimensions) - Static method in class org.anchoranalysis.mpp.points.PointClipper
- ClipHistogramMax - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Clips the input-histogram to a certain maximum value, and then delegates the calculate-level.
- ClipHistogramMax() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
- clipTo(Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Makes sure an object fits inside an extent, removing any parts which do not.
- clipTo(Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
- clipTo(T, Extent) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask
-
Ensures the element lies within a certain extent.
- close() - Method in interface org.anchoranalysis.core.progress.ProgressReporter
- close() - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
- close() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
- close() - Method in class org.anchoranalysis.core.progress.ProgressReporterMultiple
- close() - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
- close() - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
- close() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter
-
Closes any open file-handles.
- close() - Method in class org.anchoranalysis.feature.io.results.ResultsWriter
- close() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
- close() - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
- close() - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
- close() - Method in class org.anchoranalysis.plugin.image.task.slice.SharedStateSelectedSlice
- close() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
- close(boolean) - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
- close(boolean) - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
- close(boolean) - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
- close(boolean) - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
- close(boolean) - Method in interface org.anchoranalysis.experiment.log.StatefulMessageLogger
- close(boolean) - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
- close(ErrorReporter) - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
- close(ErrorReporter) - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- close(ErrorReporter) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
- close(ErrorReporter) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
- close(ErrorReporter) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
- close(ErrorReporter) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
- closeAnyOpenIO() - Method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
- closeAnyOpenIO() - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
- closestPointOnBorder(Point3d) - Method in class org.anchoranalysis.spatial.box.BoundingBox
- CODE_MINIMA - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
- CODE_PLATEAU - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
- CODE_TEMPORARY - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
- CODE_UNVISITED - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
- CoefficientOfVarianceFromAll - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
- CoefficientOfVarianceFromAll() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CoefficientOfVarianceFromAll
- coefficientOfVariation(Histogram) - Static method in class org.anchoranalysis.math.histogram.HistogramStatistics
- CoefficientOfVariation - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- CoefficientOfVariation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.CoefficientOfVariation
- CollapseFileName - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive
-
Takes a file-path of form somedir/somename.ext and converts to somedir.ext
- CollapseFileName() - Constructor for class org.anchoranalysis.plugin.quick.bean.file.path.derive.CollapseFileName
- CollectionGenerator<T> - Class in org.anchoranalysis.io.generator.collection
-
Writes a collection of elements as a subdirectory with each element as a single file in the subdirectory.
- CollectionGenerator(Generator<T>, String) - Constructor for class org.anchoranalysis.io.generator.collection.CollectionGenerator
- collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked
-
Collects the result of the operation after processing neighbor pixels
- collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor
-
Collects the result of the operation after processing neighbor pixels
- collectResult() - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute
-
Collects the result of the operation after processing neighbor pixels
- collectResult() - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
- colorAxis(Axis) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- colorChart(JFreeChart) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- ColorConverterBase - Class in org.anchoranalysis.plugin.opencv.bean.stack.provider.color
-
Converts a RGB stack into another color space using OpenCV
- ColorConverterBase() - Constructor for class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ColorConverterBase
- ColoredBase - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Base class for providers that draw entities (an outline or filled) on a background
- ColoredBase() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
- ColoredBaseWithGenerator - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Like
ColoredBasebut uses a generator to determine the colors for the objects - ColoredBaseWithGenerator() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
- ColoredMarks - Class in org.anchoranalysis.mpp.mark
- ColoredMarks - Class in org.anchoranalysis.plugin.mpp.bean.stack.provider
-
Draws a colored representation (outline or filled) of an
MarkCollectionon a background - ColoredMarks() - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
- ColoredMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
- ColoredMarks(MarkCollection, ColorIndex, IdentifierGetter<Mark>) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
- ColoredMarks(MarkCollection, ColorList) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
- ColoredMarks(Mark, RGBColor) - Constructor for class org.anchoranalysis.mpp.mark.ColoredMarks
- ColoredMarksWithDisplayStack - Class in org.anchoranalysis.mpp.io.marks
- ColoredMarksWithDisplayStack(MarksWithDisplayStack, ColorIndex, IdentifierGetter<Mark>) - Constructor for class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
- ColoredMarksWithDisplayStack(ColoredMarks, DisplayStack) - Constructor for class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
- ColoredMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Draws a colored representation (outline or filled) of a
ObjectMaskon a background - ColoredMask() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
- ColoredObjectCollection - Class in org.anchoranalysis.plugin.image.object
-
Associates a
ColorListwith aObjectCollection - ColoredObjectCollection() - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection
-
Create with an empty collection.
- ColoredObjectCollection(ObjectCollection, ColorList) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection
-
Create with an existing object and color list.
- ColoredObjectCollection(ObjectMask, RGBColor) - Constructor for class org.anchoranalysis.plugin.image.object.ColoredObjectCollection
-
Create with a single object and color.
- ColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Draws a colored representation (outline or filled) of an
ObjectCollectionon a background - ColoredObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
- coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
-
Creates colored-objects to be drawn
- coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
- coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
- coloredObjectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
- ColoredOverlayCollection - Class in org.anchoranalysis.overlay.collection
- ColoredOverlayCollection() - Constructor for class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- ColoredOverlayCollection(OverlayCollection, ColorList) - Constructor for class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- colorFor(ObjectWithProperties, int) - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
-
A color for a particular object
- colorForEachIndex(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorScheme
-
Assigns a color to each index value from a list of size
numberColors. - ColorIndex - Interface in org.anchoranalysis.core.color
- ColorIndexModulo - Class in org.anchoranalysis.core.color
- ColorIndexModulo(ColorIndex) - Constructor for class org.anchoranalysis.core.color.ColorIndexModulo
- colorLegend(LegendTitle) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- ColorList - Class in org.anchoranalysis.core.color
- ColorList() - Constructor for class org.anchoranalysis.core.color.ColorList
- ColorList(Color...) - Constructor for class org.anchoranalysis.core.color.ColorList
- ColorList(RGBColor) - Constructor for class org.anchoranalysis.core.color.ColorList
- ColorList(RGBColor...) - Constructor for class org.anchoranalysis.core.color.ColorList
- colorPlot(CategoryPlot) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- colorPlot(XYPlot) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- ColorPool - Class in org.anchoranalysis.annotation.io.assignment.generator
- ColorPool(int, ColorScheme, ColorScheme, boolean) - Constructor for class org.anchoranalysis.annotation.io.assignment.generator.ColorPool
- ColorProvider - Class in org.anchoranalysis.image.bean.provider
-
Provides a list of one or more colors
- ColorProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ColorProvider
- ColorScheme - Class in org.anchoranalysis.bean.shared.color.scheme
-
Creates a set of related colors.
- ColorScheme() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.ColorScheme
- ColorSchemeUnary - Class in org.anchoranalysis.bean.shared.color.scheme
-
Like
ColorSchemebut employs a unary operator on a call to an existingColorScheme. - ColorSchemeUnary() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
- ColorSchemeUnary(ColorScheme) - Constructor for class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
- colorSpaceCode() - Method in class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ColorConverterBase
-
The color space conversion code to use from OpenCV
- colorSpaceCode() - Method in class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ConvertRGBToHSV
- colorSpaceCode() - Method in class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ConvertRGBToLab
- column(int) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
- ColumnDefinition - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
- ColumnDefinition() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
- combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd
- combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
- combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr
- combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelAnd
- combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary
- combine(boolean, boolean) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelOr
- combine(Path, Path) - Static method in class org.anchoranalysis.bean.xml.factory.BeanPathUtilities
- Combine - Class in org.anchoranalysis.plugin.io.bean.provider.file
- Combine() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.Combine
- CombineBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
- CombineBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
- CombineCSV - Class in org.anchoranalysis.plugin.io.bean.task
- CombineCSV() - Constructor for class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- combined() - Method in class org.anchoranalysis.core.system.path.PathDifference
-
The directory-component (if it exists) and filename-component combined.
- combined() - Method in class org.anchoranalysis.core.system.path.SplitPath
- CombinedListGenerator<T> - Class in org.anchoranalysis.io.generator.combined
-
Several generators combined together with a common element-type.
- CombinedListGenerator(Stream<NameValue<Generator<T>>>) - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator
- CombinedListGenerator(NameValue<Generator<T>>) - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator
- CombinedListGenerator(Generator<T>...) - Constructor for class org.anchoranalysis.io.generator.combined.CombinedListGenerator
- CombinedName - Class in org.anchoranalysis.feature.io.name
-
A name which is unique when a primaryName is combined with a secondaryName
- CombinedName(String, String) - Constructor for class org.anchoranalysis.feature.io.name.CombinedName
-
Creates with explicit strings for both parts.
- combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AddConstantTo
- combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ConstantToThePowerOf
- combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.DivideByConstant
- combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
- combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.SubtractFrom
- combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ToThePowerOfConstant
- combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
- combineDscr(String, String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
- combineDscrsRecursively(String, String) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
-
Traverses through a set of nested-exceptions creating a description for each "combined" exception, and combining them into a single string.
- CombineObjectsForFeatures<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine
-
A way to combine (or not combine) objects so that they provide a feature-table.
- CombineObjectsForFeatures() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
- combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd
- combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
- combineSecond(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr
- combineToOnePath() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
-
Combines all the contiguous paths to a single-path
- combineToOnePath(List<ContiguousVoxelPath>) - Static method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.CombineToOnePath
-
Combines all the contiguous paths to a single-path
- CombineToOnePath - Class in org.anchoranalysis.image.core.outline.traverser.visited.combine
- combineTypes(VoxelDataType, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.datatype.CombineTypes
- CombineTypes - Class in org.anchoranalysis.image.voxel.datatype
- combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AddConstantTo
- combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ConstantToThePowerOf
- combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.DivideByConstant
- combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
- combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.SubtractFrom
- combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ToThePowerOfConstant
- combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
- combineValueAndFeature(double, double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
- CommandLineException - Exception in org.anchoranalysis.launcher
-
An exception thrown at run-time while processing command-line args
- CommandLineException(String) - Constructor for exception org.anchoranalysis.launcher.CommandLineException
- CommandLineExtracter - Class in org.anchoranalysis.launcher.options
-
Adds methods to
CommandLinefor querying and extracting options, with and without arguments. - CommandLineExtracter(CommandLine) - Constructor for class org.anchoranalysis.launcher.options.CommandLineExtracter
- CommandLineOptions - Class in org.anchoranalysis.launcher.options
-
All command-line options used by the launcher.
- common() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
-
Creates a
CommonContexta context that contains a subset of this context. - CommonContext - Class in org.anchoranalysis.core.log
-
A logger with additional configuration that are coupled together widely in the code
- CommonContext(Logger, Path) - Constructor for class org.anchoranalysis.core.log.CommonContext
- commonType(Stream<VoxelDataType>) - Static method in class org.anchoranalysis.image.voxel.datatype.FindCommonVoxelType
-
Finds a common type to represent (ideally without loss of precision} of a stream of types.
- commonType(VoxelDataType, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.datatype.FindCommonVoxelType
-
Finds a common type to represent (ideally without loss of precision} both
firstandsecond. - Comparator3d<T extends Tuple3d> - Class in org.anchoranalysis.spatial.point
- Comparator3d() - Constructor for class org.anchoranalysis.spatial.point.Comparator3d
- Comparator3i<T extends Tuple3i> - Class in org.anchoranalysis.spatial.point
- Comparator3i() - Constructor for class org.anchoranalysis.spatial.point.Comparator3i
- ComparatorOrderByName<V> - Class in org.anchoranalysis.core.identifier.name
-
Orders two name-values by their name (alphabetic order from standard String.compareTo(String))
- ComparatorOrderByName() - Constructor for class org.anchoranalysis.core.identifier.name.ComparatorOrderByName
- compare(NameValue<V>, NameValue<V>) - Method in class org.anchoranalysis.core.identifier.name.ComparatorOrderByName
- compare(T, T) - Method in class org.anchoranalysis.spatial.point.Comparator3d
- compare(T, T) - Method in class org.anchoranalysis.spatial.point.Comparator3i
- CompareAnnotations<T extends Assignment> - Class in org.anchoranalysis.plugin.annotation.bean.comparison
-
Task to compare a set of annotations to a segmentation or other set of annotations.
- CompareAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- Comparer - Class in org.anchoranalysis.annotation.io.bean.comparer
- Comparer() - Constructor for class org.anchoranalysis.annotation.io.bean.comparer.Comparer
- compareTo(WithPriority<T>) - Method in class org.anchoranalysis.core.concurrency.WithPriority
-
Orders so that
hasPriority==truehas higher priority in queue tohasPriority==false - compareTo(IndexGetter) - Method in class org.anchoranalysis.core.index.Indexable
- compareTo(MultiName) - Method in class org.anchoranalysis.feature.io.name.CombinedName
- compareTo(MultiName) - Method in class org.anchoranalysis.feature.io.name.SimpleName
- compareTo(EigenvalueAndVector) - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
- compareTo(WithConfidence<T>) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
- compareTo(SortedSetChannel) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
- compareTo(SortedSetSlice) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
- CompareWithRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
Compares a value with a range, returning specified constants if its inside the range, below it or above it
- CompareWithRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
- CompareWithRangeFeature<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range.feature
-
Like
CompareWithRangebut uses features to calculate boundary values - CompareWithRangeFeature() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
- CompatibleWithMark - Interface in org.anchoranalysis.mpp.mark
- Compose<S,T,U> - Class in org.anchoranalysis.mpp.segment.transformer
-
Combines a transformation from
StoUwith one fromUtoT - Compose() - Constructor for class org.anchoranalysis.mpp.segment.transformer.Compose
- Compose(StateTransformerBean<S, U>, StateTransformerBean<U, T>) - Constructor for class org.anchoranalysis.mpp.segment.transformer.Compose
- CompressTIFF - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod
- CompressTIFF() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CompressTIFF
- computeInitialFeasibleSolution() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
-
Compute an initial feasible solution by assigning zero labels to the workers and by assigning to each job a label equal to the minimum cost among its incident edges.
- Concatenate - Class in org.anchoranalysis.bean.define.adder
-
Concatenates a list of adders
- Concatenate - Class in org.anchoranalysis.plugin.image.bean.color.provider
- Concatenate - Class in org.anchoranalysis.plugin.image.bean.object.provider
- Concatenate - Class in org.anchoranalysis.plugin.image.bean.stack.provider
-
Combines all the channels from one or more sources (stacks, channels etc.)
- Concatenate<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Concatenates several input-managers
- Concatenate() - Constructor for class org.anchoranalysis.bean.define.adder.Concatenate
- Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
- Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
- Concatenate() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
- Concatenate() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Concatenate
- ConcatenateFileTypes - Class in org.anchoranalysis.io.generator
-
Concatenates the arrays of
FileTypethat may be returned from write operations. - ConcatenateFileTypes() - Constructor for class org.anchoranalysis.io.generator.ConcatenateFileTypes
-
Creates to always use a list for tracking.
- ConcatenateFileTypes(boolean) - Constructor for class org.anchoranalysis.io.generator.ConcatenateFileTypes
-
Create to use a list for tracking if a flag is true, otherwise to just remember the last result of each call to
ConcatenateFileTypes.add(org.anchoranalysis.io.manifest.file.FileType[]). - ConcurrencyPlan - Class in org.anchoranalysis.core.concurrency
-
How many allocated CPUS and CPUs can be used.
- ConcurrentJobMonitor - Class in org.anchoranalysis.experiment.task.processor
- ConcurrentJobMonitor(long) - Constructor for class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- ConcurrentModelException - Exception in org.anchoranalysis.core.concurrency
-
This exception indicates that an error occurred when performing inference from a model concurrently.
- ConcurrentModelException(Throwable) - Constructor for exception org.anchoranalysis.core.concurrency.ConcurrentModelException
- ConcurrentModelPool<T> - Class in org.anchoranalysis.core.concurrency
-
Keeps concurrent copies of a model to be used by different threads.
- ConcurrentModelPool(ConcurrencyPlan, ConcurrentModelPool.CreateModelForPool<T>) - Constructor for class org.anchoranalysis.core.concurrency.ConcurrentModelPool
- ConcurrentModelPool.CreateModelForPool<T> - Interface in org.anchoranalysis.core.concurrency
-
Creates a model to use in the pool
- ConditionalKernel - Class in org.anchoranalysis.image.voxel.kernel
- ConditionalKernel(BinaryKernel, int, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
- ConditionallyMergeOverlappingObjects - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
Where objects overlap, they are merged together if certain conditions are fulfilled.
- ConditionallyMergeOverlappingObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
- ConfigureBioformatsLogging - Class in org.anchoranalysis.io.bioformats
-
Singleton class for making sure Bioformats is configured configured.
- configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
- configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
- configurePermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
- ConicBase - Class in org.anchoranalysis.mpp.mark.conic
- ConicBase() - Constructor for class org.anchoranalysis.mpp.mark.conic.ConicBase
- ConicBase(MarkWithPosition) - Constructor for class org.anchoranalysis.mpp.mark.conic.ConicBase
- ConicFitterBase - Class in org.anchoranalysis.plugin.points.bean.fitter
- ConicFitterBase() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
- ConnectedComponentsFromBinarySegmentation - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Performs a binary-segmentation of the channel and converts its connected-components into objects
- ConnectedComponentsFromBinarySegmentation() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
- ConnectedComponentsFromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected
-
Converts a binary-mask into its connected components
- ConnectedComponentsFromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
- ConnectedComponentUnionFind - Class in org.anchoranalysis.image.voxel.object.factory.unionfind
- ConnectedComponentUnionFind(int, boolean) - Constructor for class org.anchoranalysis.image.voxel.object.factory.unionfind.ConnectedComponentUnionFind
- connectedTo(Contour) - Method in class org.anchoranalysis.spatial.Contour
- connectedToFirstPointOf(Contour) - Method in class org.anchoranalysis.spatial.Contour
- connectedToLastPointOf(Contour) - Method in class org.anchoranalysis.spatial.Contour
- considerVisit(Point3i, int) - Method in interface org.anchoranalysis.image.core.outline.traverser.ConsiderVisit
- considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
- considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
- considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
- considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
- considerVisit(Point3i, int, ObjectMask) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
- ConsiderVisit - Interface in org.anchoranalysis.image.core.outline.traverser
- ConsistentChannelChecker - Class in org.anchoranalysis.plugin.image.task.grouped
-
Checks that the histograms created from channels all have the same data type, res, max-value etc.
- ConsistentChannelChecker() - Constructor for class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelChecker
- ConsoleAccepted - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- ConsoleAccepted() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
- ConsoleAggregatedReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- ConsoleAggregatedReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
- ConsoleAggregatedReporter(double) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
- ConsoleMessageLogger - Class in org.anchoranalysis.experiment.log
- ConsoleMessageLogger() - Constructor for class org.anchoranalysis.experiment.log.ConsoleMessageLogger
- Constant<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
- Constant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
A constant value for thresholding
- Constant - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Always generates a constant path irrespective of the the input
- Constant - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
- Constant() - Constructor for class org.anchoranalysis.feature.bean.operator.Constant
- Constant() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
- Constant() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Constant
- Constant() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Constant
- Constant(double) - Constructor for class org.anchoranalysis.feature.bean.operator.Constant
-
Constructor with a particular value
- Constant(int) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
- Constant(String) - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Constant
- Constant(String, double) - Constructor for class org.anchoranalysis.feature.bean.operator.Constant
-
Constructor with a particular value and a custom-name
- ConstantBoundGenerator - Class in org.anchoranalysis.plugin.mpp.bean.bound
- ConstantBoundGenerator() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
- ConstantBoundGenerator(ResolvedBound) - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
- ConstantsInListFixture - Class in org.anchoranalysis.test.feature
- ConstantToThePowerOf<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
- ConstantToThePowerOf() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ConstantToThePowerOf
- ConstantWeight - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
-
All marks have weight of 1
- ConstantWeight() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ConstantWeight
- containerOptional() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
- containerRequired() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
- contains() - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
For evaluating whether this bounding-box contains other points, boxes etc.?
- contains(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
- contains(int, int, int) - Method in class org.anchoranalysis.spatial.Extent
- contains(Object) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- contains(Object) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- contains(String) - Method in interface org.anchoranalysis.bean.StringBeanCollection
- contains(String) - Method in class org.anchoranalysis.bean.StringList
- contains(String) - Method in class org.anchoranalysis.bean.StringSet
- contains(Feature<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
- contains(ChildCacheName) - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
- contains(BoundingBox) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- contains(BoundingBox) - Method in class org.anchoranalysis.spatial.Extent
- contains(Point2i) - Method in class org.anchoranalysis.spatial.Extent
- contains(Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- contains(Point3d) - Method in class org.anchoranalysis.spatial.Extent
- contains(Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- contains(Point3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
- contains(Point3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- contains(Point3i) - Method in class org.anchoranalysis.spatial.rtree.RTree
-
Which bounding-boxes contain a particular point.
- contains(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
- containsAll(Collection<?>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- containsChild(ChildCacheName) - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSource
- containsKey(Class<?>) - Method in class org.anchoranalysis.bean.BeanInstanceMap
- containsKey(Object) - Method in class org.anchoranalysis.core.value.KeyValueParams
- containsKey(String) - Method in class org.anchoranalysis.core.value.KeyValueParams
- containsMark(Mark) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- containsVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
Does the graph contain a particular vertex?
- containsX(double) - Method in class org.anchoranalysis.spatial.Extent
- containsX(int) - Method in class org.anchoranalysis.spatial.Extent
- containsY(double) - Method in class org.anchoranalysis.spatial.Extent
- containsY(int) - Method in class org.anchoranalysis.spatial.Extent
- containsZ(double) - Method in class org.anchoranalysis.spatial.Extent
- containsZ(int) - Method in class org.anchoranalysis.spatial.Extent
- context() - Method in class org.anchoranalysis.experiment.task.InputBound
- ContiguousVoxelPath - Class in org.anchoranalysis.image.core.outline.traverser.path
-
A list of visited pixels which forms one contiguous path (each voxel neighbors each other)
- ContiguousVoxelPath() - Constructor for class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
-
Without any connection-point
- ContiguousVoxelPath(Point3i, Point3i) - Constructor for class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
-
With a single initial-point, and maybe a connection point
- continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationCondition
- continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
- continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TriggerTerminationCondition
- continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
- continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
- continueIterations(int, double, int, MessageLogger) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingNumberMarks
- Contour - Class in org.anchoranalysis.spatial
-
A path of successively-neighbored points.
- Contour() - Constructor for class org.anchoranalysis.spatial.Contour
- ContourList - Class in org.anchoranalysis.plugin.points.contour
- ContourList() - Constructor for class org.anchoranalysis.plugin.points.contour.ContourList
- contoursForObject(ObjectMask) - Static method in class org.anchoranalysis.plugin.opencv.CVFindContours
- ConversionPolicy - Enum in org.anchoranalysis.image.core.channel.convert
- convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
- convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
- convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
- convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleaving
- convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
- convert(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.ChannelConvertStyle
-
Converts a particular set of channels.
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
- convert(Set<String>, ChannelGetterForTimepoint, Logger) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGB
- convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
- convert(Channel, ConversionPolicy) - Method in interface org.anchoranalysis.image.core.channel.convert.attached.ChannelConverterAttached
- convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
- convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
- convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
- convert(Channel, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverter
- convert(Channel, VoxelDataType) - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverterMulti
- convert(Stack, ConversionPolicy) - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverter
- Convert - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
Converts a channel by applying a converter (no histogram is involved in the conversion).
- Convert() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
- convert2iTo3d(List<Point2i>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- convert2iTo3f(List<Point2i>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- convert3dTo3f(List<Point3d>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- convert3fTo3d(List<Point3f>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- convert3i(List<Point3d>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- convert3i(List<Point3f>, boolean) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- convert3iTo3f(List<Point3i>) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- ConvertBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
- ConvertBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase
- ConvertChannelsInputToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack
-
An input object that converts
NamedChannelsInputtoStackSequenceInput - ConvertChannelsInputToStack(NamedChannelsInput) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
- ConvertChannelsInputToStack(NamedChannelsInput, int, Optional<String>) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
- ConvertChannelTo - Class in org.anchoranalysis.image.bean.channel.converter
-
Converts a channel from one type to another
- ConvertChannelTo() - Constructor for class org.anchoranalysis.image.bean.channel.converter.ConvertChannelTo
- ConvertChannelToWithHistogram - Class in org.anchoranalysis.image.bean.channel.converter
- ConvertChannelToWithHistogram() - Constructor for class org.anchoranalysis.image.bean.channel.converter.ConvertChannelToWithHistogram
- convertCode(int, int, EncodedVoxels, Point3i) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
-
Convert code to connected-component
- ConvertedToRuntimeException(Throwable) - Constructor for exception org.anchoranalysis.core.functional.CheckedStream.ConvertedToRuntimeException
- convertFloat(FloatBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteNoScaling
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
- convertFloat(FloatBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByType
-
Converts the current position in a
FloatBufferto the current position in aUnsignedShortBuffer. - convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
- convertFloat(FloatBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
-
Converts the current position in a
FloatBufferto the current position in aUnsignedShortBuffer. - convertFloat(FloatBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
-
Copies a value from the current position in a
FloatBufferto the current position in a buffer of typeT. - convertFrom(VoxelsWrapper, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
-
Creates a new voxels of type
Tand copies the voxels fromfrom. - ConvertFromImagePlus - Class in org.anchoranalysis.io.imagej.convert
-
Converts an
ImagePlusinto a channel or voxels. - ConvertFromMat - Class in org.anchoranalysis.plugin.opencv.convert
- ConvertFromPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
-
converts a feature to a physical distance in a XY place that is isometric
- ConvertFromPhysicalVolume() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertFromPhysicalVolume
- convertFromUnits(double, String) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits
-
Converts a value from another unit-type to base units.
- convertFromUnits(double, SpatialUnits.UnitSuffix) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits
-
Converts a value from another unit-type to base units.
- ConvertImageFormat - Class in org.anchoranalysis.plugin.image.task.bean.format
-
Converts each input-image to the default output format, optionally changing the bit depth.
- ConvertImageFormat() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
- convertIntegerBytesToFloatArray(Dimensions, ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
- convertIntegerBytesToFloatArray(Dimensions, ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
- convertIntegerBytesToFloatArray(Dimensions, ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
- ConvertNamedChannels<T extends NamedChannelsInput,S,U extends NamedChannelsInput> - Class in org.anchoranalysis.plugin.mpp.experiment.bean
-
Converts
NamedChannelsInputto a variety of others to match a delegate task - ConvertNamedChannels() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
- ConvertNamedChannelsToStack - Class in org.anchoranalysis.plugin.io.bean.input.stack
-
Manager that converts (one channel)
NamedChannelsInputtoStackSequenceInput - ConvertNamedChannelsToStack() - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
- ConvertRGBToHSV - Class in org.anchoranalysis.plugin.opencv.bean.stack.provider.color
- ConvertRGBToHSV() - Constructor for class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ConvertRGBToHSV
- ConvertRGBToLab - Class in org.anchoranalysis.plugin.opencv.bean.stack.provider.color
- ConvertRGBToLab() - Constructor for class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ConvertRGBToLab
- convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo
-
Converts a slice of single-channel into a newly created
VoxelBuffer. - convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
- convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
- convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
- convertSliceOfSingleChannel(ByteBuffer, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
- ConvertTo<T> - Class in org.anchoranalysis.io.bioformats.copyconvert
-
Converts a subset of raw voxel bytes in a
ByteBufferto one or more destination channels. - ConvertTo(Function<VoxelsWrapper, Voxels<T>>) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo
- convertTo3d(Point2d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- convertTo3i(Point2i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- convertTo3i(Point2i, int) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- ConvertToFactory - Class in org.anchoranalysis.io.bioformats.copyconvert
- ConvertToImagePlus - Class in org.anchoranalysis.io.imagej.convert
-
Converts a channel or voxels into a
ImagePlus. - ConvertToImageProcessor - Class in org.anchoranalysis.io.imagej.convert
-
Converts other voxel data-structures (as used by Anchor) to an ImageJ
ImageProcessor. - ConvertToImg - Class in org.anchoranalysis.image.voxel.convert.imglib2
- ConvertToMat - Class in org.anchoranalysis.plugin.opencv.convert
-
Converts common image data-structures used by Anchor to the
Matclass used by OpenCV. - ConvertToNativeImg - Class in org.anchoranalysis.image.voxel.convert.imglib2
- convertToObjects(Dimensions) - Method in interface org.anchoranalysis.annotation.mark.AnnotationWithMarks
-
Creates an object-collection that is a voxelized representation of the marks in the annotation.
- convertToOutputType(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
- convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertFromPhysicalVolume
- convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalAreaXY
- convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
- convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalVolume
- convertToPhysical(double, UnitConverter) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
- ConvertToPhysicalAreaXY<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
- ConvertToPhysicalAreaXY() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalAreaXY
- ConvertToPhysicalDistance<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
- ConvertToPhysicalDistance() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
- ConvertToPhysicalDistance(Feature<T>, SpatialUnits.UnitSuffix, DirectionVector) - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
- ConvertToPhysicalVolume<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
-
converts a feature to a physical distance in a XY place that is isometric
- ConvertToPhysicalVolume() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalVolume
- convertToUnits(double, String) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits
-
Converts a value in base-units to another unit-type.
- convertToUnits(double, SpatialUnits.UnitSuffix) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits
-
Converts a value in base-units to another unit-type.
- ConvertToVoxelBuffer - Class in org.anchoranalysis.io.imagej.convert
-
Converts a
ImageProcessorto a voxel-buffer of particular data-type. - ConvertUnits<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.physical
- ConvertUnits() - Constructor for class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
- convertUnsignedByte(UnsignedByteBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
- convertUnsignedByte(UnsignedByteBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByte
- convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
- convertUnsignedByte(UnsignedByteBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
- convertUnsignedByte(UnsignedByteBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
-
Copies a value from the current position in a
UnsignedByteBufferto the current position in a buffer of typeT. - convertUnsignedInt(UnsignedIntBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteNoScaling
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
- convertUnsignedInt(UnsignedIntBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByType
- convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
- convertUnsignedInt(UnsignedIntBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
- convertUnsignedInt(UnsignedIntBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
-
Copies a value from the current position in a
UnsignedIntBufferto the current position in a buffer of typeT. - convertUnsignedShort(UnsignedShortBuffer, FloatBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteNoScaling
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
- convertUnsignedShort(UnsignedShortBuffer, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByType
- convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
- convertUnsignedShort(UnsignedShortBuffer, UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
- convertUnsignedShort(UnsignedShortBuffer, T) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
-
Copies a value from the current position in a
UnsignedShortBufferto the current position in a buffer of typeT. - convertValue(short) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
- convertValue(short) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromSignedShort
- convertValue(short) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromUnsignedShort
- ConvertWithHistogram - Class in org.anchoranalysis.plugin.image.bean.channel.provider.convert
-
Converts a channel to a different voxel data-type by applying a converter with an associated histogram.
- ConvertWithHistogram() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
- convexHull2D(List<Point2i>) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities
-
Like
ConvexHullUtilities.convexHull2D(List, int)but uses a default minimum number of points. - convexHull2D(List<Point2i>, int) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities
-
Apply a convex-hull algorithm to filter a set of points.
- ConvexHull2D - Class in org.anchoranalysis.plugin.points.bean.mask.provider
-
Sets particular voxels to high only if they exist on the convex-hull of the outline of a mask.
- ConvexHull2D() - Constructor for class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHull2D
- ConvexHull3D - Class in org.anchoranalysis.plugin.points.bean.mask.provider
- ConvexHull3D() - Constructor for class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHull3D
- ConvexHullBase - Class in org.anchoranalysis.plugin.points.bean.mask.provider
- ConvexHullBase() - Constructor for class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
- ConvexHullUtilities - Class in org.anchoranalysis.plugin.points.convexhull
- copyAllChannels(Dimensions, ByteBuffer, DestinationChannelForIndex, int, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo
-
Copies the channels in the source buffer into a particular
DestinationChannelForIndex. - copyAllFrames(IFormatReader, List<Channel>, ProgressReporter, ImageFileShape, ConvertTo<?>, ReadOptions) - Static method in class org.anchoranalysis.io.bioformats.copyconvert.CopyConvert
-
Copies all frames, channels, z-slices (in a byte-array) into a destination set of Channels converting them if necessary along the way
- copyBufferIndexTo(T, int, T, int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
- copyChange(MarkCollection) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.MarksFromPartition
-
Makes a copy, with different marks
- copyChangeIterationsDilation(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
-
Copies the bean setting an new value for
iterationsDilation - copyChangeParams(KeyValueParams) - Method in class org.anchoranalysis.feature.energy.EnergyStack
- CopyConvert - Class in org.anchoranalysis.io.bioformats.copyconvert
-
Copies the bytes from a
IFormatReaderto a list of channels, converting if necessary. - CopyFilesExperiment - Class in org.anchoranalysis.plugin.io.bean.experiment
- CopyFilesExperiment() - Constructor for class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- CopyFilesMethod - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod
- CopyFilesMethod() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CopyFilesMethod
- CopyFilesNaming - Interface in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
- CopyFilesNamingOne - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
- CopyFilesNamingOne() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
- CopyFilesNamingOneRegEx - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
- CopyFilesNamingOneRegEx() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
- copyFrom(int, int, ResultsVector, int) - Method in class org.anchoranalysis.feature.results.ResultsVector
-
Copies a contiguous subset of results from another vector
- copyFrom(VoxelsWrapper, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
-
Copies voxels from a source (of any type) to voxels of type
T. - copyFromFloat(Voxels<FloatBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
-
Copies voxels from a source of type @{link FloatBuffer} to voxels of type
T. - copyFromUnsignedByte(Voxels<UnsignedByteBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
-
Copies voxels from a source of type @{link UnsignedByteBuffer} to voxels of type
T. - copyFromUnsignedInt(Voxels<UnsignedIntBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
-
Copies voxels from a source of type @{link UnsignedIntBuffer} to voxels of type
T. - copyFromUnsignedShort(Voxels<UnsignedShortBuffer>, Voxels<T>) - Method in class org.anchoranalysis.image.voxel.convert.VoxelsConverter
-
Copies voxels from a source of type @{link UnsignedShortBuffer} to voxels of type
T. - copyInit(Class<?>, NamedProviderStore<S>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine
-
Copies objects of a particular class from the define AND initializes
- copyObjectsFrom(NamedProvider<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- copyPixelsTo(int, BoundingBox, Voxels<UnsignedByteBuffer>, BoundingBox) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
-
Copies pixels on a particular channel to an output buffer
- copyProvider(Class<?>, NamedProviderStore<T>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine
-
Copies objects of a particular class from the define AND initializes as a provider
- copyStackCollectionFrom(NamedProvider<Stack>) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- copyTo(NameValueSet<Feature<T>>) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
- copyToDirectory(File) - Method in class org.anchoranalysis.test.TestLoader
-
Copies all the data in the test-data folder (recursively), preserving file-dates
- copyToDirectory(String[], File) - Method in class org.anchoranalysis.test.TestLoader
-
Copies specific subdirectories from the test-data folder (recursively), preserving file-dates
- copyToDuplicate(NameValueSet<Feature<T>>) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
- copyVoxelsTo(ObjectMask, VoxelsWrapper, BoundingBox) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- copyVoxelsTo(BoundingBox, VoxelsWrapper, BoundingBox) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- copyWithoutInit(Class<?>, NamedProviderStore<S>) - Method in class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine
-
Copies objects of a particular class from the define WITHOUT doing any initialization
- cornerMin() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
- cornerMin() - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
The bottom-left corner of the bounding box.
- CostMatrix<T> - Class in org.anchoranalysis.annotation.io.assignment
-
Stores costs between all possible pairings between elements from two lists.
- CostOverlapWithinMidpointDistance - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
TODO the center-of-gravity calculation can be turned into a FeatureCalculation which is cacheable
- CostOverlapWithinMidpointDistance() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
- count() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
- count() - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
- count() - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate
-
Counts the number of values satisfying the predicate - across all voxels.
- Count - Class in org.anchoranalysis.feature.bean.results
-
The number of the results from a particular feature.
- Count - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
Counts the number of items in a histogram (posssibly in relation to a threshold: above, below etc.)
- Count() - Constructor for class org.anchoranalysis.feature.bean.results.Count
- Count() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
- countAtPosition(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernel
- countAtPosition(int, Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
-
This method is deliberately not broken into smaller pieces to avoid inlining.
- countByte(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingBounded
-
Counts all voxels in the intersection of two bounded-voxels of type
BoundedVoxelsthat match a predicate. - countByteMasked(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, PredicateTwoBytes) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingBounded
-
Counts all voxels intersection of two bounded-voxels of type
BoundedVoxelsbut only voxels that lie on an object-mask and match a predicate. - CountEqual - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
- CountEqual() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
- Counter - Class in org.anchoranalysis.math.arithmetic
-
A simple counter that increments
- Counter() - Constructor for class org.anchoranalysis.math.arithmetic.Counter
- countForObject(ObjectMask) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
- countForObject(ObjectMask) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
- countForObject(ObjectMask) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate
-
Counts the number of values satisfying the predicate - but restricted to voxels corresponding to on in an object-mask.
- countIntersectingVoxels() - Method in class org.anchoranalysis.mpp.overlap.MaxIntensityProjectionPair
- countIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- countIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Counts the number of intersecting-voxels between two object-masks.
- countIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingObjects
-
Counts the number of intersecting-voxels between two object-masks.
- CountKernel - Class in org.anchoranalysis.image.voxel.kernel.count
- CountKernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernel
- CountKernelNeighborhood - Class in org.anchoranalysis.image.voxel.kernel.count
-
For every voxel on the outline, count ALL neighbors that are adjacent, including those lying outside the scene.
- CountKernelNeighborhood(boolean, BinaryValuesByte, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhood
- CountKernelNeighborhoodBase - Class in org.anchoranalysis.image.voxel.kernel.count
-
The number of touching-faces of a voxel with a neighbor
- CountKernelNeighborhoodBase(boolean, BinaryValuesByte, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
- CountKernelNeighborhoodIgnoreOutsideScene - Class in org.anchoranalysis.image.voxel.kernel.count
-
For every voxel on the outline, count ALL neighbors that are adjacent, but ignoring any outside the scene.
- CountKernelNeighborhoodIgnoreOutsideScene(boolean, BinaryValuesByte, boolean, Extent, ReadableTuple3i) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodIgnoreOutsideScene
- CountKernelNeighborhoodMask - Class in org.anchoranalysis.image.voxel.kernel.count
-
The number of touching-faces of a voxel with a neighbor, so long as the neighbor is part of an object-mask
- CountKernelNeighborhoodMask(boolean, BinaryValuesByte, ObjectMask, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask
- countOff() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- countOn() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- countThreshold(RelationToThreshold) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
- countThreshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
- countThreshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
- countThreshold(RelationToValue, double) - Method in class org.anchoranalysis.math.histogram.Histogram
- CountVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting
-
Like
IterateVoxelsBoundingBoxbut counts voxels matching a predicate rather than iterating. - CountVoxelsIntersectingObjects - Class in org.anchoranalysis.image.voxel.iterator.intersecting
-
Like
CountVoxelsIntersectingBoundedbut specifically counts areas of intersection between twoObjectMasks. - CoupledManifests - Class in org.anchoranalysis.plugin.io.manifest
- CoupledManifests(Manifest, DeserializedManifest, Logger) - Constructor for class org.anchoranalysis.plugin.io.manifest.CoupledManifests
- CoupledManifests(DeserializedManifest, int, Logger) - Constructor for class org.anchoranalysis.plugin.io.manifest.CoupledManifests
- CoupledManifestsInputManager - Class in org.anchoranalysis.plugin.io.bean.input.manifest
- CoupledManifestsInputManager() - Constructor for class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
- create() - Method in interface org.anchoranalysis.bean.provider.Provider
- create() - Method in class org.anchoranalysis.bean.provider.ProviderHolder
- create() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProvider
- create() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
- create() - Method in class org.anchoranalysis.bean.shared.random.RandomNumberGeneratorBean
- create() - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
- create() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
- create() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
- create() - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
- create() - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
- create() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
- create() - Method in class org.anchoranalysis.bean.shared.StringMap
- create() - Method in class org.anchoranalysis.feature.bean.list.Define
- create() - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed
- create() - Method in class org.anchoranalysis.feature.bean.list.DefineSingle
- create() - Method in class org.anchoranalysis.feature.bean.list.FeatureListProvider
- create() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
- create() - Method in class org.anchoranalysis.feature.bean.list.ParametersAsFeatures
- create() - Method in class org.anchoranalysis.feature.bean.list.PrependName
- create() - Method in class org.anchoranalysis.feature.bean.list.SelectFromShared
- create() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProvider
- create() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
- create() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
- create() - Method in class org.anchoranalysis.image.bean.interpolator.ImgLib2Lanczos
- create() - Method in class org.anchoranalysis.image.bean.interpolator.ImgLib2Linear
- create() - Method in class org.anchoranalysis.image.bean.interpolator.InterpolatorBean
- create() - Method in class org.anchoranalysis.image.bean.interpolator.None
- create() - Method in class org.anchoranalysis.image.bean.provider.ChannelProvider
- create() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
- create() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
- create() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
- create() - Method in class org.anchoranalysis.image.bean.provider.ColorProvider
- create() - Method in class org.anchoranalysis.image.bean.provider.DimensionsProvider
- create() - Method in class org.anchoranalysis.image.bean.provider.HistogramProvider
- create() - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
- create() - Method in class org.anchoranalysis.image.bean.provider.MaskProvider
- create() - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
- create() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProvider
- create() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
- create() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
- create() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProvider
- create() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
- create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
- create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
- create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkFactory
- create() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkPointListFactory
- create() - Method in class org.anchoranalysis.mpp.bean.provider.MarkBoundsProvider
- create() - Method in class org.anchoranalysis.mpp.bean.provider.MarkCollectionProvider
- create() - Method in class org.anchoranalysis.mpp.bean.provider.SingleMarkProvider
- create() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreator
- create() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
- create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
- create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
- create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
- create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
- create() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- create() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
- create() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
- create() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
- create() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.GuessDimensions
- create() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
- create() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
- create() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
- create() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
- create() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
- create() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
- create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
- create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
- create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Empty
- create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
- create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
- create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
- create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
- create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference
- create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
- create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
- create() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
- create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
- create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
- create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
- create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
- create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
- create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
- create() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
- create() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
- create() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
- create() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
- create() - Method in interface org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder.CreateFirstSecondOrder
- create() - Method in class org.anchoranalysis.plugin.imagej.bean.interpolator.InterpolatorBeanImageJ
- create() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderLDAClassifier
- create() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
- create() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
- create() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsReference
- create() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
- create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.CreateNew
- create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
- create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
- create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
- create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
- create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
- create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
- create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
- create() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RetrieveSingleMarkOnly
- create() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
- create() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
- create() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- create() - Method in class org.anchoranalysis.spatial.rotation.factory.RotationMatrixFactory
-
Creates a
RotationMatrix. - create() - Static method in class org.anchoranalysis.test.feature.ConstantsInListFixture
-
creates a feature-list associated with the fixture
- create(boolean) - Method in interface org.anchoranalysis.core.concurrency.ConcurrentModelPool.CreateModelForPool
-
Creates a model
- create(boolean, Supplier<T>) - Static method in class org.anchoranalysis.bean.OptionalFactory
-
Creates only if a boolean flag is true, otherwise returns empty.
- create(int) - Method in class org.anchoranalysis.image.core.object.label.DecodeLabels
-
Creates a list of elements from voxels that are labelled with unique integers (sequentially increasing)
- create(int) - Method in interface org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactory
- create(int) - Method in class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactoryHistogramReuse
- create(int) - Method in class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitonFactoryHistogram
- create(BufferedImage) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.CreateStackFromBufferedImage
- create(Class<? extends FeatureInput>) - Method in interface org.anchoranalysis.feature.calculate.cache.CacheCreator
- create(Class<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.session.cache.creator.CacheCreatorSimple
- create(String) - Static method in class org.anchoranalysis.bean.OptionalFactory
-
Creates
Optional.empty()for an empty string, or otherwise Optional.of - create(String) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
-
Creates an Optional from a string that might be empty or null
- create(String, Optional<ManifestDescription>, OutputterChecked, String) - Static method in class org.anchoranalysis.io.generator.text.TextFileOutputter
-
Creates a
TextFileOutput. - create(Path) - Static method in class org.anchoranalysis.io.generator.tabular.CSVWriter
-
Creates and starts a CSVWriter (it's always allowed, so will never return null)
- create(Iterator<T>, Optional<AxisLimits>, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.bean.Plot
-
Creates a graph
- create(Iterator<T>, Optional<AxisLimits>, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.LinePlot
- create(List<Point3d>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory
- create(List<Point3d>, int) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory
- create(List<Point3i>) - Static method in class org.anchoranalysis.image.core.object.factory.SingleObjectFromPointsFactory
- create(List<T>) - Method in interface org.anchoranalysis.bean.xml.factory.CreateFromList
- create(List<T>, List<T>, boolean, CheckedToDoubleBiFunction<T, T, CreateException>) - Static method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
-
Creates by calculating the cost between elements.
- create(List<V>, Function<V, ObjectMask>, Extent, boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborGraph
-
Create the graph with object-masks as vertices, where edges represent the number of intersecting voxels between objects.
- create(Map<Integer, T>, UnaryOperator<T>) - Method in class org.anchoranalysis.image.core.object.label.DecodeLabels
-
Creates a map of elements to other elements that are labelled with unique integers (sequentially increasing) in voxels.
- create(Optional<String>, String) - Static method in class org.anchoranalysis.feature.io.name.MultiNameFactory
-
Creates either a multi-name that is either has a single part or a double part.
- create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.AddToDefaults
- create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.NoneExcept
- create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnabledRules
-
Creates rules for determining whether an output is enabled or disabled.
- create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.Permissive
- create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
- create(Optional<MultiLevelOutputEnabled>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
-
Deprecated.
- create(IFormatReader, VoxelDataType, int) - Static method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertToFactory
- create(Provider<T>) - Static method in class org.anchoranalysis.bean.OptionalFactory
-
Creates from a provider if non-null.
- create(SharedObjects) - Static method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsInitParams
- create(SharedObjects) - Static method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
- create(Logger, Path) - Static method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
-
Creates empty params
- create(FeatureList<T>, SharedFeatureSet<T>) - Method in interface org.anchoranalysis.feature.session.cache.FeatureSessionCacheFactory
- create(FeatureList<T>, SharedFeatureSet<T>) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCacheFactory
- create(FeatureList<T>, SharedFeatureSet<T>) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCacheFactory
- create(FeatureCSVMetadata, Outputter) - Static method in class org.anchoranalysis.feature.io.csv.FeatureCSVWriter
-
Maybe creates a
FeatureCSVWriterdepending if the output is allowed. - create(ImageInitParams, SharedObjects) - Static method in class org.anchoranalysis.mpp.bean.init.PointsInitParams
- create(Channel) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
- create(Channel) - Static method in class org.anchoranalysis.image.core.stack.DisplayStack
- create(Channel, Mask) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
- create(Channel, ObjectCollection) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
- create(Channel, ObjectMask) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
- create(Dimensions, VoxelDataType) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
-
Creates an empty initialized channel for a particular data-type
- create(RGBStack) - Static method in class org.anchoranalysis.image.core.stack.DisplayStack
- create(Stack) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.BufferedImageFactory
- create(Stack) - Static method in class org.anchoranalysis.image.core.stack.DisplayStack
- create(BinaryVoxels<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
- create(VoxelBuffer<?>) - Static method in class org.anchoranalysis.image.voxel.statistics.HistogramFactory
- create(SliceBufferIndex<T>) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
- create(SliceBufferIndex<T>, VoxelDataType) - Method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
- create(ObjectCollection, Extent, boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborGraph
-
Create the graph with object-masks as vertices, where edges represent the number of intersecting voxels between objects.
- create(Voxels<?>) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
- create(Voxels<?>, Optional<Resolution>) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
- create(Voxels<?>, Optional<Resolution>) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
- create(VoxelsWrapper) - Static method in class org.anchoranalysis.image.voxel.statistics.HistogramFactory
- create(VoxelsWrapper, Optional<ObjectMask>) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
- create(InputManagerParams) - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
- create(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Combine
- create(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
- create(InputManagerParams) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
- create(InputOutputContext, Optional<Define>, Optional<? extends InputForMPPBean>) - Static method in class org.anchoranalysis.mpp.io.input.MPPInitParamsFactory
- create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.LoggingDestination
-
Creates a logger for this destination
- create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf
- create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
- create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToConsole
- create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToMultiple
- create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToTextFile
- create(OutputterChecked, ErrorReporter, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.ToTextFileOnlyIfFailure
- create(Mark) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
- create(Mark, EnergyStackWithoutParams, RegionMap) - Static method in class org.anchoranalysis.mpp.mark.voxelized.memo.PxlMarkMemoFactory
- create(Mark, EnergyStackWithoutParams, RegionMap) - Static method in class org.anchoranalysis.mpp.mark.voxelized.VoxelizedMarkFactory
- create(Extent, VoxelDataType) - Method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
- create(CommandLine, Path, Path, Path) - Static method in class org.anchoranalysis.launcher.executor.ExperimentExecutorFactory
-
Creates an experiment-executor from a command line that EITHER: uses a default-experiment OR accepts a path passed as the first command-line argument
- createAddCriteria() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceFirstAndSecond
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceRatioFirstAndSecond
- createAggregateFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.SubtractReducedFromMerged
- createAndStartSession() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
- createArguments(CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig
- createAscending() - Static method in class org.anchoranalysis.test.feature.plugins.HistogramFixture
-
a histogram from 0 to 255 (inclusive) where each bin is equal to its index (value 5 has count 5, value 100 has count 100 etc.)
- createAssignment(ObjectCollection, ObjectCollection, double, Dimensions) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentObjectFactory
- createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner
- createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
- createAssignment(ObjectsToCompare, Dimensions, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
- createAsStack() - Method in class org.anchoranalysis.image.bean.provider.ChannelProvider
- createAsStack() - Method in class org.anchoranalysis.image.bean.provider.MaskProvider
- createAsStack() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProvider
- createAsStack() - Method in interface org.anchoranalysis.image.core.stack.ProviderAsStack
-
Creates from the image-bean in the form of a stack
- createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
- createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
- createAxisArray() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientXY
- createBackground(NamedProviderStore<Stack>, String) - Static method in class org.anchoranalysis.mpp.io.output.BackgroundCreator
- createBean(Class<?>, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
- createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.define.DefineFactory
- createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.IncludeBeanFactory
- createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.IncludeListFactory
- createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.IndirectlyFromListBeanFactory
- createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.ListBeanFactory
- createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.ReplacePropertyBeanFactory
- createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.StringListFactory
- createBean(Class, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.StringSetFactory
- createBeanInstance(Class<?>, BeanDeclaration) - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
- createBetweenTwoPoints(Point3d, Point3d) - Static method in class org.anchoranalysis.image.core.orientation.DirectionVector
- createBetweenTwoPoints(Point3i, Point3i) - Static method in class org.anchoranalysis.image.core.orientation.DirectionVector
- createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in interface org.anchoranalysis.image.bean.nonbean.spatial.arrange.ArrangeStack
- createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
- createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Single
- createBoundingBoxesOnPlane(Iterator<RGBStack>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
- createBufferedImage() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- createBufferedImage(int, int) - Method in class org.anchoranalysis.plot.PlotInstance
- createBufferedImageBBox(BoundingBox) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- createByte() - Method in class org.anchoranalysis.image.core.mask.Mask
- createByte() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
- createByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory
-
Create voxels-extracter for
UnsignedByteBuffer. - createByte(Voxels<UnsignedByteBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory
-
Create voxels-assigner for
UnsignedByteBuffer. - createByte(BoundingBox) - Static method in class org.anchoranalysis.image.voxel.BoundedVoxelsFactory
- createByte(Extent, IntFunction<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory
-
Create voxels-arithmethic for
UnsignedByteBuffer - createCachedCalculationForDerived(CalculationResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
- createCachedCalculationForDerived(CalculationResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
- createCachedCalculationForDerived(CalculationResolver<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
- createCalculator(CreateCalculatorHelper, ImageInitParams, BoundReplaceStrategy<FeatureInputStack, ? extends ReplaceStrategy<FeatureInputStack>>) - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
- createChannel() - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
- createChannel(int, boolean) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- createChannelDuplicate(int) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- createChannelDuplicateForBoundingBox(int, BoundingBox) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- createChart(DefaultCategoryDataset, String, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.BarPlot
-
Creates a chart
- createChart(DefaultBoxAndWhiskerCategoryDataset, String, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.BoxPlot
- createChart(XYDataset, String, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.LinePlot
-
Creates a chart
- createChart(S, String, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
- createCollection(Channel, ObjectCollection, CalculateLevel, int, MessageLogger) - Static method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollectionFactory
- createColor(ColoredMarks, RegionMembershipWithFlags) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory
- createColors(int) - Method in class org.anchoranalysis.annotation.io.assignment.generator.ColorPool
- createCombinedContour() - Method in class org.anchoranalysis.plugin.points.contour.ContourList
- createCombinedException(String, Throwable) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
- CreateCombinedStack - Class in org.anchoranalysis.image.bean.nonbean.init
- createConnectedComponents(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
- createConverter() - Method in class org.anchoranalysis.image.bean.channel.converter.ConvertChannelTo
- createConverter() - Method in class org.anchoranalysis.image.bean.channel.converter.ConvertChannelToWithHistogram
- createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
- createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
- createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
- createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByTypeToByte
- createConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ToByte
- createCountKernelMask(ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
- createDataset(Iterator<T>) - Method in class org.anchoranalysis.plot.index.LinePlot
- createDataset(Iterator<T>) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
- createDataset(Iterator<T>) - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
-
Creates a sample dataset
- createDefaultDataset() - Method in class org.anchoranalysis.plot.index.BarPlot
- createDefaultDataset() - Method in class org.anchoranalysis.plot.index.BoxPlot
- createDefaultDataset() - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
- createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
- createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
- createDelegate(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
- createDescending() - Static method in class org.anchoranalysis.test.feature.plugins.HistogramFixture
- createDescriptor(Extent) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
- createDesignMatrix(List<Point3f>) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
- createDestinationFile(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CopyFilesMethod
- createDilatedObject(ObjectMask, Optional<Extent>, boolean, int, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation
-
Dilates an object-mask, growing the bounding-box as necessary.
- createDilationKernel(BinaryValuesByte, Optional<Voxels<UnsignedByteBuffer>>, int) - Method in class org.anchoranalysis.image.voxel.object.morphological.DilationKernelFactory
- createDim() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
- createDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
- createDims() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
-
Returns the dimensions or null if none are provided
- createDistanceMapForMask(Mask, boolean, double, double, boolean, boolean) - Static method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
- createDistanceMapForVoxels(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>, boolean, double, double, boolean, boolean) - Static method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
- createDocumentBuilder() - Static method in class org.anchoranalysis.bean.xml.XmlUtilities
- createDuplicatePxlMarkMemoList() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- CreateEllipse - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
- CreateEllipse() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
- createEmptyInitialised(Dimensions) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
- createEmptyInitialisedToSupportMaxValue(Dimensions, long) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
-
Creates an empty initialized channel with discrete type with as minimal as needed data-type to support a maximum value
- createEmptyMat(Extent, int) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat
- createEmptyOff(Extent) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory
-
Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to off (0).
- createEmptyOff(Extent, VoxelDataType) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory
-
Creates an empty binary-voxels of a particular data-type with all voxels initialized to OFF (0)
- createEmptyOn(Extent) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory
-
Creates binary-voxels using unsigned 8-bit byte type and with all voxels set to ON (255)
- createEmptyUninitialised(Dimensions) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
- createEnergyStack(ImageInitParams, Logger) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
- createErodedObject(ObjectMask, Optional<Extent>, boolean, int, boolean, Optional<AcceptIterationConditon>) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalErosion
- CreateException - Exception in org.anchoranalysis.core.exception
- CreateException(String) - Constructor for exception org.anchoranalysis.core.exception.CreateException
- CreateException(String, AnchorCombinableException) - Constructor for exception org.anchoranalysis.core.exception.CreateException
- CreateException(String, HasFriendlyErrorMessage) - Constructor for exception org.anchoranalysis.core.exception.CreateException
- CreateException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.CreateException
- createExperimentExecutor(CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig
- createExperimentOutputter(String, Manifest, RecordedOutputsWithRules, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.OutputManager
-
Creates an outputter for the experiment in general.
- createExperimentState() - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
- createExperimentState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
- createFeatureCalcParams(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- createFeatureCalcParams(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueIndividualEnergyGreaterThan
- createFeatureCalcParams(Mark, RegionMap, EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueMarkGreaterEqualThan
- CreateFeatureInput<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session
- createFeatureList(String, TestLoader) - Static method in class org.anchoranalysis.test.feature.plugins.FeaturesFromXmlFixture
- createFeatureNames() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
- createFeatureNames() - Method in interface org.anchoranalysis.image.feature.session.FeatureTableCalculator
-
Creates A list of names for each feature (columns of the table)
- createFeatureNames() - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
- createFeatureNames() - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
- createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
-
Creates features that will be applied on the objects.
- createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
- createFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, NamedFeatureStoreFactory, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
- createFeatures(NamedFeatureStore<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
- createFeatureSession() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
-
Creates session for evaluating
featureoptionally adding an energy-stack. - createFeatureSession(UnaryOperator<FeatureList<T>>, SharedObjects) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator
-
Creates session for evaluating
features. - createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
- createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
- createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in interface org.anchoranalysis.io.output.writer.Writer
-
The path to write a particular output to.
- createFilenameForWriting(String, String, Optional<ManifestDescription>) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors
-
The path to write a particular output to.
- createFileOutputFor(String, FeedbackBeginParameters<VoxelizedMarksWithEnergy>, String) - Static method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterUtilities
- createFitResultFromMatrixAandCenter(DoubleMatrix2D, DoubleMatrix2D, boolean) - Static method in class org.anchoranalysis.plugin.points.bean.fitter.EllipsoidFitHelper
- createFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory
-
Create voxels-extracter for
FloatBuffer - createFloat(Voxels<FloatBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory
-
Create voxels-assigner for
FloatBuffer. - createFloat(Extent, IntFunction<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory
-
Create voxels-arithmethic for
FloatBuffer - createForBuffer(VoxelBuffer<T>, Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
- createForDirectoryPermissive(Path, boolean) - Static method in class org.anchoranalysis.io.output.outputter.OutputterChecked
-
Creates, defaulting to a permissive output-manager in a a particular directory.
- createForFeature(Feature<?>) - Method in interface org.anchoranalysis.feature.session.CreateFeatureInput
- createForFeatures(List<NamedBean<FeatureListProvider<T>>>, LabelHeaders, ResultsWriterOutputNames, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
-
Alternative static constructor that creates a shared-state from a list of named feature-providers
- createForFeatures(ResultsWriterOutputNames, FeatureTableCalculator<T>, LabelHeaders, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
-
Alternative static constructor that creates a shared-state from a feature-store
- createForFeatures(NamedFeatureStore<T>, LabelHeaders, ResultsWriterOutputNames, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
-
Alternative static constructor that creates a shared-state from a feature-store
- createForSingle(AnchorBean<?>, String) - Static method in class org.anchoranalysis.bean.permute.setter.PermutationSetterUtilities
-
Searches through a list of property fields to find one that matches the propertyName
- createForSubdirectory(String) - Method in class org.anchoranalysis.test.TestLoader
-
Creates a new test-loader for a subdirectory of the current test
- createFrom(int, ObjectMask) - Method in interface org.anchoranalysis.image.core.object.label.DecodeLabels.CreateElementFromScaledObject
- createFrom(int, ObjectMask) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask
-
Creates an element of type
Tfrom an object-representation and index. - createFrom3Vecs(DoubleMatrix1D, DoubleMatrix1D, DoubleMatrix1D) - Static method in class org.anchoranalysis.spatial.rotation.RotationMatrix
- createFromChannel(Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.MinimumFilter
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.Invert
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Duplicate
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.Sobel
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractCenterSlice
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MaximumIntensityProjection
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MeanIntensityProjection
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.EdgeFilterIJ
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter3D
- createFromChannel(Channel) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
- createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor
- createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.MeanFilter2D
- createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.VarianceFilter2D
- createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter2D
- createFromChannel(Channel, int) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
- createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
- createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeObjectIntensity
- createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.IdentifyObjects
- createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
- createFromChannel(Channel, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
- createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase
- createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase
- createFromChannelWithConstant(Channel, double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
- createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
- createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
- createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
- createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
- createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
- createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.AllValuesOff
- createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.AllValuesOn
- createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
- createFromDimensions(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
- createFromExistingCollections(InputOutputContext, Optional<Define>, Optional<NamedProvider<Stack>>, Optional<NamedProvider<ObjectCollection>>, Optional<KeyValueParams>) - Static method in class org.anchoranalysis.mpp.io.input.MPPInitParamsFactory
- createFromExplicitDirectory(String) - Static method in class org.anchoranalysis.test.TestLoader
-
Creates a new test-data loader using an explicit File path as root
- createFromExplicitDirectory(Path) - Static method in class org.anchoranalysis.test.TestLoader
-
Creates a new test-data loader using an explicit File path as root
- createFromFile(Path) - Method in class org.anchoranalysis.io.manifest.directory.sequenced.DeriveElementsFromSequencedDirectory
-
Creates an element of type
Tfrom a one particular file in the sequence. - createFromFile(Path) - Method in class org.anchoranalysis.io.manifest.directory.sequenced.SequencedDirectoryDeserializer
- createFromFlag(boolean, Supplier<T>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
-
Creates an
Optionalfrom a boolean flag - createFromFlag(boolean, T) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
-
Creates an
Optionalfrom a boolean flag - createFromFlagChecked(boolean, CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
-
Creates an
Optionalfrom a boolean flag - where the supplier can thrown an exception - createFromFlagOptional(boolean, Supplier<Optional<T>>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
- createFromHistogram(Histogram) - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
- createFromHistogram(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
- createFromHistogram(Histogram) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
- createFromList(List<T>, Function<T, BoundingBox>) - Static method in class org.anchoranalysis.spatial.box.BoundedList
-
Creates for a list, minimally fitting a bounding-box around all elements
- CreateFromList<T> - Interface in org.anchoranalysis.bean.xml.factory
- createFromMarks(MarkCollection, KernelCalculationContext, Logger) - Static method in class org.anchoranalysis.plugin.mpp.segment.optimization.VoxelizedMarksWithEnergyFactory
- createFromMask(Mask) - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMask
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Duplicate
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.FitBoxToOnVoxels
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.FlattenZ
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
- createFromMask(Mask) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
- createFromMask(Mask, Mask) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHull2D
- createFromMask(Mask, Mask) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHull3D
- createFromMask(Mask, Mask) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
- createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
- createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
- createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
- createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
- createFromMaskedChannel(Channel, Mask) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.ZeroOutsideMask
- createFromMavenWorkingDirectory() - Static method in class org.anchoranalysis.test.TestLoader
-
Creates a new test-data loader finding "src/test/resources" using the Maven working directory
- createFromMavenWorkingDirectory(String) - Static method in class org.anchoranalysis.test.TestLoader
-
Creates a new test-data loader finding "src/test/resources/PLUS_SOMETHING" using the Maven working directory
- createFromNotObjects(ObjectCollection, Dimensions, BinaryValues) - Static method in class org.anchoranalysis.image.core.mask.MaskFromObjects
-
We look for space NOT in the objects, and create channel to display it
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.RejectIfNotConnected
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Duplicate
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeature
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.SortByFeature
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.NotInContainer
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZ
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZWithinContainer
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.FlattenZ
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.DrawLineAlongConvexHull
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
- createFromObjects(ObjectCollection) - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
- createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Filter
- createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
- createFromObjects(ObjectCollection, Optional<ObjectCollection>, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
- createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
- createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
- createFromObjects(ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
- createFromObjects(ObjectCollection, Dimensions, BinaryValues) - Static method in class org.anchoranalysis.image.core.mask.MaskFromObjects
-
We look for space IN objects, and create channel to display it
- createFromOutputter(String, OutputterChecked) - Static method in class org.anchoranalysis.io.generator.tabular.CSVWriter
-
Creates and starts a CSVWriter if it's allowed, otherwise returns
Optional.empty(). - createFromOverlays(ColoredOverlayCollection, IdentifierGetter<Overlay>, IdentifierGetter<ObjectWithProperties>) - Static method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributesFactory
- createFromSource(Channel) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
- createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromChannel
- createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
- createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
- createFromSource(Channel) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
- createFromStack(Stack) - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
- createFromStack(Stack) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
- createFromStack(Stack) - Method in class org.anchoranalysis.plugin.opencv.bean.stack.provider.color.ColorConverterBase
- createFromString(String) - Static method in class org.anchoranalysis.spatial.axis.AxisTypeConverter
-
Maps a string of x, y, z (case ignored) to a corresponding axis type
- createFromTupleDuplicate(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.Extent
-
Createss an extent from a point (duplicating the point for internal use)
- createFromTupleReuse(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.Extent
-
Creates from a point that is reused internally (without duplication)
- createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.And
- createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
-
Creates masks from some combination of two masks
- createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.IfHighLow
- createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Or
- createFromTwoMasks(Mask, Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Xor
- createGrayscaleByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.BufferedImageFactory
- createGroupMap(ConsistentChannelChecker) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
-
Creates a map for the storing an aggregate-data-object for each group.
- createGroupMap(ConsistentChannelChecker) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
- createGroupMap(ConsistentChannelChecker) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
- createHashMapToId() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- createHeaders() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- createHeaders() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
- createHeaders(boolean) - Method in class org.anchoranalysis.plugin.image.task.feature.GenerateLabelHeadersForCSV
-
Creates the label-headers (the headers for columns not associated with features)
- createHistogramIgnoreZero(Channel, ObjectMask, boolean) - Static method in class org.anchoranalysis.image.core.object.HistogramFromObjectsFactory
- createIdArr() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- createIdHashMap() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- createImageDim() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForMPP
- createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
- createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
- createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
- createInitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
- createInitialized(Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
- createInitParams(Optional<SharedObjects>, Optional<EnergyStack>) - Static method in class org.anchoranalysis.image.feature.session.InitParamsHelper
- createInitParams(InputOutputContext) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
- createInitParams(InputOutputContext, Optional<NamedProvider<Stack>>, Optional<NamedProvider<ObjectCollection>>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
- createInitParams(InputForMPPBean, InputOutputContext) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
- createInputContext() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
-
Creates an input-context, reusing parameters from the experiment-execution
- createInputProcessContext(Optional<String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
- createInputProcessContext(Optional<String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
- createInt() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
- createInt(Voxels<UnsignedIntBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory
-
Create voxels-extracter for
UnsignedIntBuffer - createInt(Voxels<UnsignedIntBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory
-
Create voxels-assigner for
UnsignedIntBuffer. - createInt(BoundingBox) - Static method in class org.anchoranalysis.image.voxel.BoundedVoxelsFactory
- createInt(Extent, IntFunction<UnsignedIntBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory
-
Create voxels-arithmethic for
UnsignedIntBuffer - createIntersectionComplement(ColoredOverlayCollection, ColoredOverlayCollection) - Static method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- createInverted() - Method in class org.anchoranalysis.image.core.mask.Mask
- createInverted() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
-
Inverts the values so OFF becomes ON, and vice-versa
- createKernelFactoryNames() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- createKeyValueParams() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
-
returns the associated KeyValueParams or an empty set, if no params are associated with the energyScheme
- createLabelledChannel(BoundedList<T>, Optional<Map<Integer, T>>) - Method in class org.anchoranalysis.image.core.object.label.LabelObjects
-
Creates a channel that contains a unique integer (label) for each element's object-representation.
- createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorScheme
-
Creates a list of colors of particular size.
- createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
- createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromList
- createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromSingle
- createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.HSB
- createList(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.VeryBright
- createListChildFeatures() - Method in class org.anchoranalysis.feature.bean.Feature
-
Returns a list of Features that exist as bean-properties of this feature, either directly or in lists.
- createListMembershipWithFlags() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
- createManifestDescription() - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
- createManifestDescription() - Method in class org.anchoranalysis.io.generator.serialized.KeyValueParamsGenerator
- createManifestDescription() - Method in class org.anchoranalysis.io.generator.serialized.SerializedGenerator
- createManifestDescription() - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
- createManifestDescription() - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
- createManifestDescription() - Method in class org.anchoranalysis.io.generator.tabular.CSVGenerator
- createManifestDescription() - Method in class org.anchoranalysis.io.generator.text.StringGenerator
- createManifestDescription() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksAsUniqueValueGenerator
- createManifestDescription() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
- createManifestDescription(String) - Static method in class org.anchoranalysis.io.generator.collection.CollectionGenerator
- createMap(OpenedRaster) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.Autoname
- createMap(OpenedRaster) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
- createMap(OpenedRaster) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromMetadata
- createMap(OpenedRaster) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
- createMapToIndex() - Method in class org.anchoranalysis.feature.name.FeatureNameList
-
Creates a map from the feature-names to their indices in the list
- createMarkEllipsoidLeastSquares(CheckedSupplier<List<Point3i>, CreateException>, Dimensions, boolean, double) - Static method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.EllipsoidFactory
- createMarkEllipsoidLeastSquares(ObjectMask, Dimensions, boolean, double) - Static method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.EllipsoidFactory
-
Creates a MarkEllipsoid using least-squares fitting to the points on the outline of an object-mask
- createMarkFromPoint(Point3d, int, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.MarkConicFactory
- createMarkFromPoint(Point3i, int, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.MarkConicFactory
- CreateMarkFromPoints - Class in org.anchoranalysis.mpp.bean.points
- CreateMarkFromPoints() - Constructor for class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
- createMarkFromPoints3f(List<Point3f>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory
- createMarkFromPoints3i(List<Point3i>) - Static method in class org.anchoranalysis.mpp.mark.points.PointListFactory
- createMaskOff(Dimensions) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to OFF
- createMaskOff(Dimensions, BinaryValues) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to OFF
- createMaskOn(Dimensions) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to ON
- createMaskOn(Dimensions, BinaryValues) - Static method in class org.anchoranalysis.image.core.mask.MaskFactory
-
Creates a binary-mask for specific dimensions with all voxels set to ON
- createMerged(ColoredMarks) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- createMerged(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- createMerged(OverlayCollection) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- createMessageForDscr(String) - Method in exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
- createMessageForDscr(String) - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
- createMessageForDscr(String) - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
-
Creates a message for the exception from the description
- createMessageForDscr(String) - Method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
- createMinusOne() - Method in class org.anchoranalysis.spatial.Extent
-
Creates a new Extent with each dimension decreased by one
- createMockFeatureWithCalculation() - Static method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture
-
Creates a mock-feature (using a mock-FeatureCalculation under the hood) which counts the number of pixels in an object
- createMockFeatureWithCalculation(ToDoubleFunction<T>) - Static method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture
-
Creates a mock-feature (using a mock-FeatureCalculation under the hood) with a result calculated using a lambda
- createModelPool(ConcurrencyPlan) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentStackIntoObjectsPooled
-
Creates the model pool (to be used by multiple threads)
- createModelPool(ConcurrencyPlan) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
- createModelPool(ConcurrencyPlan) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
- createNamedFeatureList(List<NamedBean<FeatureListProvider<T>>>) - Method in class org.anchoranalysis.feature.list.NamedFeatureStoreFactory
-
Create a list of na
- createNamedFeatureProviders(String, TestLoader) - Static method in class org.anchoranalysis.test.feature.plugins.FeaturesFromXmlFixture
- createNames() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- createNecessaryDirectories(Path) - Static method in class org.anchoranalysis.annotation.io.WriterUtilities
- CreateNew - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
Creates a new channel with all values initialized to a constant (by default zero)
- CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
- CreateNew - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
-
Creates a new empty collection of marks
- CreateNew() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
- CreateNew() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.CreateNew
- CreateNew() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.CreateNew
- createNewMarkPos(Orientation2D, Ellipse, RandomNumberGenerator, Dimensions, double, double, boolean) - Static method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
- createNext(int, int) - Method in interface org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement.TableCreator
- createNullErrorReporter() - Static method in class org.anchoranalysis.core.log.LogUtilities
- createObject(Mask) - Static method in class org.anchoranalysis.image.core.object.factory.SingleObjectFromChannelFactory
- createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
- createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
- createObject(DrawOverlay, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.Overlay
- createObjects() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
- createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.Comparer
- createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.AnnotationMarksComparer
- createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MarksComparer
- createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
- createObjects(Path, Dimensions, boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.ObjectComparer
- createOneToMany(Generator<T>, CheckedFunction<S, Stream<T>, ?>) - Static method in class org.anchoranalysis.io.generator.GeneratorBridge
-
Creates a bridge that maps ONE-TO-MANY from source to destination (i.e.
- createOneToOne(Generator<T>, CheckedFunction<S, T, ?>) - Static method in class org.anchoranalysis.io.generator.GeneratorBridge
-
Creates a bridge that maps ONE-TO-ONE from source to destination (i.e.
- createOrderProvider() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
- createOrderProvider() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
- createOrderProvider() - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
- createOrderProvider() - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
- createOrReuse(Throwable) - Static method in exception org.anchoranalysis.core.exception.InitException
- createOrReuse(T) - Method in class org.anchoranalysis.feature.session.strategy.replace.AlwaysNew
- createOrReuse(T) - Method in class org.anchoranalysis.feature.session.strategy.replace.CacheAndReuseStrategy
- createOrReuse(T) - Method in interface org.anchoranalysis.feature.session.strategy.replace.ReplaceStrategy
- createOrReuse(T) - Method in class org.anchoranalysis.feature.session.strategy.replace.ReuseSingletonStrategy
- createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendCsv
- createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendFilePath
- createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
- createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
- createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendMarks
- createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendObjects
- createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
- createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
- createOutPathString() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
- createPair(CreateCalculatorHelper, ImageInitParams, CacheTransferSourceCollection) - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
- createPairsUnique() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- createPairsUnique() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
- createParam(String, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
- createParams(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelFaces
- createParams(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxels
- createParams(boolean, boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
- createParamsForImage(EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.KeyValueParamsForImageCreator
- createPathDeriver(String, String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
-
Creates a (rooted) file-path generator for a rootName and a regEx which matches three groups The first group should correspond to top-level folder for the project The second group should correspond to the unique name of the dataset.
- createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
- createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
- createPayloadCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
-
Determines the payload for any given or potential vertex
- createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
- createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
- createPermutedFeaturesFor(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
- createPolicy() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase
- createPrecalc(DrawOverlay, ObjectWithProperties, Dimensions) - Static method in class org.anchoranalysis.overlay.writer.DrawOverlay
- createPrefixerContext() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
- createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
- createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
- createPrioritizer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
-
Determines the priority (and selection criteria) used to allow merges between neighbors
- createPriority(ObjectVertex, ObjectVertex, Logger) - Method in interface org.anchoranalysis.plugin.image.object.merge.priority.Prioritizer
- CreateProposalVisualization - Interface in org.anchoranalysis.mpp.proposer.visualization
- CreateProposeVisualizationList - Class in org.anchoranalysis.mpp.proposer.visualization
- CreateProposeVisualizationList() - Constructor for class org.anchoranalysis.mpp.proposer.visualization.CreateProposeVisualizationList
- createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
- createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- createRadiiArray() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
- createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- createRadiiArrayResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- createRasters(AnnotationWithMarks, DisplayStack, Path, ColorScheme, Path, Logger, boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
- createReducedFeature(Feature<FeatureInputPairObjects>, Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
- createRGB(Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Voxels<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.BufferedImageFactory
- createRGBMaskGenerator(DrawObject, DisplayStack, ColorList) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
- createRGBStack(Channel, Channel, Channel, VoxelDataType) - Static method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
- createRoot() - Static method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
- createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.Orientation
- createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
- createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
- createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
- createRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
- createRow(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
- createSameSize(ChannelProvider, String, Channel) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker
-
Creates a new channel from a provider, making sure it's the same size as an an existing channel
- createSameSize(MaskProvider, String, Channel) - Static method in class org.anchoranalysis.plugin.image.channel.DimensionsChecker
-
Creates a new channel from a provider, making sure it's the same size as an an existing channel
- createScaledMask(DrawOverlay, ObjectWithProperties, double, Object, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.object.scaled.FromMask
- createScaledMask(DrawOverlay, ObjectWithProperties, double, Object, Dimensions, BinaryValuesByte) - Method in interface org.anchoranalysis.overlay.object.scaled.ScaledMaskCreator
-
Creates a scaled-version of the mask
- createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
- createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
- createScaleObject(DrawOverlay, double, ObjectWithProperties, Overlay, Dimensions, Dimensions, BinaryValuesByte) - Method in class org.anchoranalysis.overlay.Overlay
- createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.AddToDefaults
- createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.NoneExcept
- createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
-
Creates a new second-level
SingleLevelOutputEnabledfrom the relevant set of strings. - createSecondLevelFromSet(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
- createSequence(VoxelDataType) - Method in class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
- createSession() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
- createSet() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- createSet() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- createSet() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- createSetter(AnchorBean<?>) - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty
- createSetter(AnchorBean<?>) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
- createSetter(AnchorBean<?>) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
- createSharedState(LabelHeaders, List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>, ResultsWriterOutputNames, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- createSharedState(LabelHeaders, List<NamedBean<FeatureListProvider<S>>>, ResultsWriterOutputNames, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
- createSharedState(LabelHeaders, List<NamedBean<FeatureListProvider<U>>>, ResultsWriterOutputNames, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
- createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
-
Creates a shared-state for the duration of a particular input-job
- createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
-
Sets a new output-sequence for the series
- createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- createSharedStateJob(InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- createShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.extracter.VoxelsExtracterFactory
-
Create voxels-extracter for
UnsignedShortBuffer. - createShort(Voxels<UnsignedShortBuffer>, int) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory
-
Create voxels-assigner for
UnsignedShortBuffer. - createShort(Extent, IntFunction<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmeticFactory
-
Create voxels-arithmethic for
UnsignedShortBuffer - createSingle(CreateCalculatorHelper, ImageInitParams, BoundReplaceStrategy<FeatureInputSingleObject, CacheAndReuseStrategy<FeatureInputSingleObject>>) - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
- createSingle(T, Function<T, BoundingBox>) - Static method in class org.anchoranalysis.spatial.box.BoundedList
-
Creates for a single element, using its current bounding-box.
- createStack(List<RGBStack>, ChannelFactorySingleType) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.RasterArranger
- CreateStackFromBufferedImage - Class in org.anchoranalysis.image.core.stack.bufferedimage
- createStackSequenceForSeries(int) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
- createStatistics() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
- createStatistics() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
- createStatistics() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- createStatistics() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.mpp.bean.mark.MarkRegion
- createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- createStatisticsFor(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.MaxNonZero
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
- createStatisticsFor(VoxelizedMark, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Specific
- createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
- createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
- createStatisticsForBBox(VoxelizedMark, Dimensions, BoundingBox, int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
- createStatisticsHeaderNames() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
- createStatisticsHeaderNames() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
- createStatisticsHeaderNames() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
-
The headers needed to create statistics
- createSubdirectory(String, ManifestDirectoryDescription, boolean) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors
-
Maybe creates a subdirectory for writing to.
- createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
- createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
- createSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in interface org.anchoranalysis.io.output.writer.Writer
-
Maybe creates a subdirectory for writing to.
- createSubset(IntPredicate) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- createSubset(List<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
-
A subset of the collection identified by particular indices.
- createSubsetFromIDs(IntPredicate) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- createUninitialised(Dimensions, VoxelDataType) - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
- createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
- createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
- createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
- createUninitialized(Extent) - Static method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
- createUninitialized(Extent) - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
- createUniqueNamesSorted() - Method in class org.anchoranalysis.feature.name.FeatureNameList
- createValues() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- createValues() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
- createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
- createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.DirectionVectorBean
-
Creates a vector in a particular direction
- createVector() - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
- createVector3d() - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
- createWithConsoleFallback(OutputterChecked, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.LoggingDestination
-
Creates a logger for this destination - and if anything goes wrong reporting fallback into the console.
- createWithDir(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CompressTIFF
- createWithDir(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.CopyFilesMethod
- createWithDir(Path, Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.SimpleCopy
- createWithLogFallback(OutputterChecked, MessageLogger, ExperimentExecutionArguments, boolean) - Method in class org.anchoranalysis.experiment.bean.log.LoggingDestination
-
Creates a logger for this destination - and if anything goes wrong reporting fallback into a log.
- createWithoutColor(ObjectCollection, IdentifierGetter<ObjectMask>) - Static method in class org.anchoranalysis.overlay.collection.OverlayCollectionObjectFactory
- createWithoutColor(MarkCollection, RegionMembershipWithFlags) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory
- createWithPrefix(DirectoryWithPrefix, MultiLevelOutputEnabled, OutputWriteSettings, Optional<WriteOperationRecorder>, Optional<MultiLevelRecordedOutputs>, boolean) - Static method in class org.anchoranalysis.io.output.outputter.OutputterChecked
-
Creates a bound output-manager from an existing
OutputManagerwith a prefix. - createWithRangeLimits(Iterator<T>, Optional<AxisLimits>) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
- createWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.BioformatsWriter
-
Creates or gets an instance of
IFormatWriterwhich dictates the file format to use for writing. - createWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMETiff
- createWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMEXML
- createWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.Tiff
- cross(Vector3d, Vector3d) - Static method in class org.anchoranalysis.spatial.point.Vector3d
- CSVGenerator<T> - Class in org.anchoranalysis.io.generator.tabular
- CSVGenerator(String) - Constructor for class org.anchoranalysis.io.generator.tabular.CSVGenerator
- CSVReporterAggregated - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
Outputs statistics on current energy / kernel acceptance etc.
- CSVReporterAggregated() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
- CSVReporterBest - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
Outputs a CSV with statistics on the configuration/energy only the best configuration state changes.
- CSVReporterBest() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
- CSVReporterUtilities - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- CSVRow - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv
-
A row of the CSV File
- CSVRow(ColumnDefinition) - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
- csvString() - Method in class org.anchoranalysis.math.histogram.Histogram
- CSVWriter - Class in org.anchoranalysis.io.generator.tabular
- CUBIC_MICRO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
- CUBIC_NANO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
- currentStateDescription() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- currentTemperature() - Method in class org.anchoranalysis.mpp.bean.anneal.AnnealScheme
- currentTemperature() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
- currentTemperature() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.NoAnnealing
- customizeExperimentTemplate(ExperimentExecutor, CommandLine) - Method in class org.anchoranalysis.launcher.config.LauncherConfig
- CustomManagerFromPath - Class in org.anchoranalysis.launcher.executor.selectparam.path
-
Loads a custom-manager from a path
- CustomManagerFromPath(Path) - Constructor for class org.anchoranalysis.launcher.executor.selectparam.path.CustomManagerFromPath
- CutBelowThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
-
This cuts a Histogram below a threshold BUT TRANSFERS ALL THE COUNT greater than equal to the threshold into the bin just below the threshold value
- CutBelowThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
- CVFindContours - Class in org.anchoranalysis.plugin.opencv
-
Wrapper around Open CV's findContours function
- CVInit - Class in org.anchoranalysis.plugin.opencv
-
Provides for initialization of the JavaCPP bridge to OpenCV.
D
- dataType() - Method in class org.anchoranalysis.image.core.channel.factory.ChannelFactorySingleType
- dataType() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
-
Data-type of each voxel in the buffer.
- dataType() - Method in interface org.anchoranalysis.image.voxel.factory.VoxelsFactoryTypeBound
- dataType() - Method in class org.anchoranalysis.image.voxel.Voxels
- DataTypeMaxIntensity<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity
-
The maximum-intensity allowed by the data-type of the stack (e.g.
- DataTypeMaxIntensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.DataTypeMaxIntensity
- DebugDependentProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor
-
Executes different processors depending on whether we are in debug mode or not
- DebugDependentProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
- decode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
-
Decodes a chain-code into a point
- decodeConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
- DecodeLabels<T> - Class in org.anchoranalysis.image.core.object.label
-
Decodes a labelled raster into derived objects or object-like elements.
- DecodeLabels(Voxels<?>, int, int, DecodeLabels.CreateElementFromScaledObject<T>) - Constructor for class org.anchoranalysis.image.core.object.label.DecodeLabels
- DecodeLabels.CreateElementFromScaledObject<T> - Interface in org.anchoranalysis.image.core.object.label
-
Creates an element from the scaled-object and its index
- DecomposeIntoConnectedComponents - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected
-
Ensures each object in a collection is a connected-component, decomposing it if necessary into multiple objects.
- DecomposeIntoConnectedComponents() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
- decrement() - Method in class org.anchoranalysis.math.arithmetic.Counter
- decrementX() - Method in class org.anchoranalysis.spatial.point.Tuple3i
- decrementX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- decrementY() - Method in class org.anchoranalysis.spatial.point.Tuple3i
- decrementY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- decrementZ() - Method in class org.anchoranalysis.spatial.point.Tuple3i
- decrementZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- deepCopy() - Method in class org.anchoranalysis.core.color.ColorList
- deepCopy() - Method in class org.anchoranalysis.feature.energy.EnergyTotal
- deepCopy() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
- deepCopy() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
-
Make a deep copy (except the
energySchemewhich is reused). - deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
-
Creates a deep-copy of the marks
- deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
- deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- deepCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
- deepCopy() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- deepCopy() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- deepCopy() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
- deepCopy() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- Default - Class in org.anchoranalysis.io.bioformats.bean.options
- Default() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.Default
- DEFAULT_COLOR_SET_GENERATOR - Static variable in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
- DEFAULT_FUNC_NUM_PIXELS - Static variable in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture
- DEFAULT_IMAGE_INPUT_NAME - Static variable in class org.anchoranalysis.mpp.io.input.MultiInput
- defaultColorIndexFor(int) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
- defaultExperimentOrCustom(CommandLine, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.experiment.ExperimentFactory
-
Chooses either a path to the default-experiment or a path to a custom experiment.
- DefaultFindChildStrategy - Class in org.anchoranalysis.feature.session.strategy.child
-
The default strategy for finding children by always directly taking (or creating a child-cache) as necessary.
- DefaultInstance - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates a default bean-instance is available.
- defaultOutputs() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
- defaultOutputs() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
-
If specified, default rules for determine which outputs are enabled or not.
- defaultOutputs() - Method in class org.anchoranalysis.experiment.bean.task.Task
-
If specified, default rules for determine which outputs are enabled or not.
- defaultOutputs() - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
-
If specified, default rules for determine which outputs are enabled or not.
- defaultOutputs() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
- defaultOutputs() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
- defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
- defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
- defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
- defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
- defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
- defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
- defaultOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- defaultOutputs() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
- defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
- defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
- defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
- defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
- defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
- defaultOutputs() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
- Define - Class in org.anchoranalysis.bean.define
-
A bean where the definitions of many different
NamedBeans can be specified. - Define<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
- Define() - Constructor for class org.anchoranalysis.bean.define.Define
- Define() - Constructor for class org.anchoranalysis.feature.bean.list.Define
- Define(List<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.Define
- Define(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.list.Define
- DefineAdder - Interface in org.anchoranalysis.bean.define.adder
-
Adds bean-definitions to a Define class
- DefineAdderBean - Class in org.anchoranalysis.bean.define.adder
- DefineAdderBean() - Constructor for class org.anchoranalysis.bean.define.adder.DefineAdderBean
- DefineAdderUtilities - Class in org.anchoranalysis.bean.define.adder
- DefineAdderWithPrefixBean - Class in org.anchoranalysis.bean.define.adder
-
Adds a prefix
- DefineAdderWithPrefixBean() - Constructor for class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
- DefinedNamed<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
- DefinedNamed() - Constructor for class org.anchoranalysis.feature.bean.list.DefinedNamed
- DefineFactory - Class in org.anchoranalysis.bean.define
-
Creates a new Define
- DefineFactory() - Constructor for class org.anchoranalysis.bean.define.DefineFactory
- DefineOutputter - Class in org.anchoranalysis.mpp.segment.bean.define
-
After using applying a
Defineon inputs, output produced entities (images, histograms, objects etc.) - DefineOutputter() - Constructor for class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
- DefineOutputterImage - Class in org.anchoranalysis.mpp.segment.bean.define
-
Helper for tasks that uses a
Definein association with an input to execute some tasks, and then outputs results * - DefineOutputterImage() - Constructor for class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterImage
- DefineOutputterMPP - Class in org.anchoranalysis.mpp.segment.bean.define
- DefineOutputterMPP() - Constructor for class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP
- DefineOutputterMPP.OperationWithInitParams<T> - Interface in org.anchoranalysis.mpp.segment.bean.define
- DefineOutputterMPPWithEnergy - Class in org.anchoranalysis.plugin.mpp.bean.define
-
Like a
Definebut outputs also MPP-related data objects and an energy-stack. - DefineOutputterMPPWithEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterMPPWithEnergy
- DefineOutputterMPPWithEnergy.OperationWithEnergyStack<T,S> - Interface in org.anchoranalysis.plugin.mpp.bean.define
- DefineOutputterWithEnergy - Class in org.anchoranalysis.plugin.mpp.bean.define
- DefineOutputterWithEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
- DefineSingle<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
- DefineSingle() - Constructor for class org.anchoranalysis.feature.bean.list.DefineSingle
- delegate() - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
- delete(Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationDeleter
-
Deletes all files at this path (or any other paths derived from this one
- delete(Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationDeleter
- delete(Path) - Method in class org.anchoranalysis.annotation.io.SimpleAnnotationDeleter
- delete(BoundingBox, T) - Method in class org.anchoranalysis.spatial.rtree.RTree
- DensityKernel - Class in org.anchoranalysis.image.voxel.kernel.density
- DensityKernel(int, BinaryValuesByte, double) - Constructor for class org.anchoranalysis.image.voxel.kernel.density.DensityKernel
- deriveArray() - Method in class org.anchoranalysis.spatial.Extent
-
Derives an three-element array with each dimension in the extent.
- deriveAssociatedFiles() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
- deriveBoundingBox() - Method in class org.anchoranalysis.spatial.box.PointRange
- deriveBoundingBoxNoCheck() - Method in class org.anchoranalysis.spatial.box.PointRange
-
Like
PointRange.deriveBoundingBox()but doesn't throw an exception if no points exist. - deriveConnectedByte(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.factory.unionfind.ConnectedComponentUnionFind
-
Converts binary-voxels (byte) into connected components.
- deriveConnectedInt(BinaryVoxels<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.object.factory.unionfind.ConnectedComponentUnionFind
-
Converts binary-voxels (int) into connected components.
- DerivedObject - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
- DerivedObject() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
- DeriveElementsFromSequencedDirectory<T> - Class in org.anchoranalysis.io.manifest.directory.sequenced
-
Derives elements of type
Tfrom a directory containing a sequence of files. - DeriveElementsFromSequencedDirectory(SequencedDirectory) - Constructor for class org.anchoranalysis.io.manifest.directory.sequenced.DeriveElementsFromSequencedDirectory
- deriveExtent() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
- deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
- deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
- deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
- deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
- deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
- deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.CollapseFileName
- deriveFrom(Path, boolean) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
- deriveFromDelegate(FeatureInputSingleObject, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
- deriveFromDelegate(T, U) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
- DeriveFromPair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
Embeds each feature in a
FeatureDeriveFromPairfeature (first, second or merge) and prepends with a string. - DeriveFromPair() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
- deriveInputsStartBatch(ObjectCollection, EnergyStack, boolean, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
-
Derives a list of inputs (i.e.
- deriveLabels(T, int) - Method in interface org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects.LabelsForInput
-
Calculates labels for a given input (and index)
- deriveName(File, int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.FromOutputName
- deriveName(File, int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
- deriveName(File, int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.NormalizedPath
- deriveName(File, int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RegExMatcher
- deriveName(Collection<File>, String, Logger) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.patternspan.PatternSpan
- deriveName(Collection<File>, String, Logger) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
- deriveObject() - Method in interface org.anchoranalysis.image.core.object.seed.Seed
- deriveObject() - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
- deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.mark.Mark
-
Create an object-mask representation of the mark (i.e.
- deriveObject(Dimensions, RegionMembershipWithFlags, BinaryValuesByte) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
- deriveObject(BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
- deriveObject(BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
- deriveObject(BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate
-
Creates an object-mask for all the voxels inside the bounding-box satisfying the predicate.
- deriveObjects() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- deriveObjects(Dimensions, RegionMembershipWithFlags) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- derivePath(DerivePath, Path) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.PathFromGenerator
- derivePointsLocal() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Creates a list of all ON voxels as points, using local coordinates i.e.
- deriveRootedPath(Path, String, boolean, boolean) - Static method in class org.anchoranalysis.plugin.io.input.path.RootedFilePathUtilities
- deriveScore(double, double, FeatureResultSupplier) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
- deriveScore(double, double, FeatureResultSupplier) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
-
Derive scores given the value, mean and standard-deviation
- deriveScore(double, double, FeatureResultSupplier) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.ZScore
- deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
- deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
- deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
- deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
- deriveScoreFromVoxel(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
- deriveStack(boolean) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
-
Derives a
Stackfrom the display-stack that will be converted to 8-bit if necessary. - deriveStackDuplicate() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MeanAcrossObjects
- deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
- deriveStatistic(DoubleArrayList) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
- deriveSubdirectory(String, ManifestDirectoryDescription, boolean) - Method in class org.anchoranalysis.io.output.outputter.Outputter
- deriveSubdirectory(String, ManifestDirectoryDescription, Optional<SubdirectoryBase>, boolean) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
-
Derives a bound-output-manager for a (possibly newly created) subdirectory of the existing manager
- deriveUnsignedBytePredicate() - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes
-
Derives a predicate with a different interface for operating on
UnsignedByteBuffer. - deriveUnsignedByteProcessor() - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes
-
Derives a processor with a different interface for operating on
UnsignedByteBuffer. - describe() - Method in class org.anchoranalysis.launcher.executor.selectparam.path.CustomManagerFromPath
- describe() - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam
-
A string that can be displayed to the user to describe this particular
SelectParam. - describe() - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
- describe() - Method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
- describe() - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph
-
Generates a string describing the entire graph (vertices and edges)
- describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannels
- describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
- describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
- describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
- describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
- describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer
-
Returns a string summarizing this item
- describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
- describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
- describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
- describe() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
- describe(boolean) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
Describes the graph in a multi-line string.
- describe(String) - Method in class org.anchoranalysis.plugin.io.summarizer.FrequencyMap
- describeAcceptedClasses() - Method in interface org.anchoranalysis.bean.initializable.property.PropertyDefiner
- describeAcceptedClasses() - Method in class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
- describeBean() - Method in class org.anchoranalysis.bean.AnchorBean
-
A (maybe longer) description identifying the bean and perhaps its key parameters.
- describeBean() - Method in class org.anchoranalysis.feature.bean.Feature
- describeBean() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- describeBean() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
- describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
- describeBean() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
- describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
- describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
- describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
- describeBean() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
- describeBean() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
- describeBean() - Method in class org.anchoranalysis.mpp.feature.mark.MarkPairCollection
- describeBean() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
- describeBean() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
- describeBean() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
- describeBean() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
- describeChildren() - Method in class org.anchoranalysis.bean.AnchorBean
-
Generates a string describing the children of the current bean.
- describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph
-
Generates a string to describe a potential merge
- describeEdge(ObjectVertex, ObjectVertex, ObjectVertex, double, boolean) - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger
- DescribeGraph - Class in org.anchoranalysis.plugin.image.object.merge
-
Logs descriptions of the graph
- DescribeGraph(NeighborGraph, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.DescribeGraph
-
Constructor
- describeLast() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
- describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
- describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
- describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
- describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
- describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
- describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
- describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
- describeLast() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
- describeMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.DescribeGraph
- describeMerge(ObjectVertex, TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger
- describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
- describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
- describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
- describeNoun() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannels
- describeParams() - Method in class org.anchoranalysis.feature.bean.Feature
- describeParams() - Method in class org.anchoranalysis.feature.bean.operator.Constant
- describeParams() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
- describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
- describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
- describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
- describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
- describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
- describeParams() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
- describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
- describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsMark
- describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
- describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
- describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
- describeParams() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
- describeParams() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
- describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
- describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
- describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
- describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
- describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
- describeParams() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
- describePropertiesFriendly() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
-
A string that uniquely identifies all properties in the bean, but friendly to humans
- describeTo(boolean) - Method in class org.anchoranalysis.core.graph.TypedEdge
-
Describes the edge by showing the to vertex, and optionally the payload.
- description() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
-
A description of this directory for the manifest.
- description(String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch
-
Match a file whose manifest-description has a specific function.
- description(String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DirectoryMatch
- description(String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch
-
Match a file whose manifest-description has a specific function and type.
- description(String, String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch
-
Match a file whose manifest-description has either of two specific function and a specific type.
- descriptionAndOutputName(String, String, String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch
-
Match a file whose manifest-description has either of two specific function and a specific type and whose output-name matches a specific value.
- descriptionForList(String) - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
-
A string description of all the items of the list concatenated together with a character in between
- descriptionLong() - Method in class org.anchoranalysis.feature.bean.Feature
- descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Constant
- descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Reference
- descriptionLong() - Method in class org.anchoranalysis.feature.bean.operator.Sum
- descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.AbsoluteValue
- descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
- descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
- descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Multiply
- descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.list.MeanGeometric
- descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.NormalizedRange
- descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
- descriptionLong() - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
- DescriptionMatch - Class in org.anchoranalysis.io.manifest.finder.match
- descriptionWithCustomName() - Method in class org.anchoranalysis.feature.bean.Feature
- DescriptiveNameContainsImageLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
- DescriptiveNameContainsImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
- DeserializationFailedException - Exception in org.anchoranalysis.core.serialize
- DeserializationFailedException(Exception) - Constructor for exception org.anchoranalysis.core.serialize.DeserializationFailedException
- DeserializationFailedException(String) - Constructor for exception org.anchoranalysis.core.serialize.DeserializationFailedException
- DeserializationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.serialize.DeserializationFailedException
- deserialize(Path) - Method in interface org.anchoranalysis.core.serialize.Deserializer
- deserialize(Path) - Method in class org.anchoranalysis.core.serialize.KeyValueParamsDeserializer
- deserialize(Path) - Method in class org.anchoranalysis.core.serialize.ObjectInputStreamDeserializer
- deserialize(Path) - Method in class org.anchoranalysis.core.serialize.XStreamDeserializer
- deserialize(Path) - Method in class org.anchoranalysis.mpp.io.marks.MarkCollectionDeserializer
- DeserializedManifest - Class in org.anchoranalysis.plugin.io.manifest
-
A manifest after being deserialized from the file-system.
- DeserializedManifest(File, ManifestDeserializer) - Constructor for class org.anchoranalysis.plugin.io.manifest.DeserializedManifest
- deserializeManifest(File) - Method in interface org.anchoranalysis.io.manifest.deserializer.ManifestDeserializer
- deserializeManifest(File) - Method in class org.anchoranalysis.io.manifest.deserializer.SimpleManifestDeserializer
- Deserializer<T> - Interface in org.anchoranalysis.core.serialize
- DestinationChannelForIndex - Interface in org.anchoranalysis.io.bioformats
-
Selects a destination-channel for the byte-copier, given an index
- destinationPath(Path, Path, File, int) - Method in interface org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNaming
-
Returns the output path (destination to to be copied to) for a given single file
- destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
- destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
- destinationPathRelative(Path) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.RemoveWhitespace
- destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.ApplyRegExSubstitution
- destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
- destinationPathRelative(Path, String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.EnsureRegExMatch
- destinationPathRelative(Path, Path, File, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
- destinationPathRelative(Path, Path, File, int) - Method in interface org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNaming
-
Calculates the relative-output path (to be appended to destDir)
- destinationPathRelative(Path, Path, File, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
- destinationPathRelative(Path, Path, File, int) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.PreserveName
- determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
- determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
-
Returns a list of channel-names or null if they are unavailable
- determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
- determineChannelNames(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.SwitchChannelTime
- determineCost() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
-
Merges
- determineInputType(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType
-
Finds a common input-type for two classes, throwing an exception if the two types aren't compatible.
- determineInputType(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType
-
Finds a common input-type for classes in the list, throwing an exception if any two types aren't compatible.
- Develop - Class in org.anchoranalysis.plugin.mpp.experiment.bean.define
-
Derives various types of outputs (images, histograms etc.) from
MultiInputs. - Develop() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
- Difference - Class in org.anchoranalysis.plugin.image.feature.bean.score
- Difference() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.Difference
- DifferenceCalculateLevelStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
Similar to
Differencebut calculates the width as the standard-deviation of the histogram - DifferenceCalculateLevelStandardDeviation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
- differenceFrom(Path, Path) - Static method in class org.anchoranalysis.core.system.path.PathDifference
-
Finds the difference between a path and a base
- dilate(boolean, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
Grow bounding-box by 1 pixel in all directions
- dilate(BinaryVoxels<UnsignedByteBuffer>, boolean, int, Optional<Voxels<UnsignedByteBuffer>>, int, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation
- dilate(BinaryVoxels<UnsignedByteBuffer>, int, Optional<Voxels<UnsignedByteBuffer>>, int, Optional<AcceptIterationConditon>, DilationKernelFactory) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalDilation
-
Performs a morpholgical dilation operation
- Dilate - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
-
Performs an dilation morphological operation on a binary-image
- Dilate - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
-
Dilates each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
- Dilate() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
- Dilate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
- DilationKernel3 - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
- DilationKernel3(BinaryValuesByte, boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3
- DilationKernel3ZOnly - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
- DilationKernel3ZOnly(BinaryValuesByte, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3ZOnly
- DilationKernelFactory - Class in org.anchoranalysis.image.voxel.object.morphological
- DilationKernelFactory(SelectDimensions, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.object.morphological.DilationKernelFactory
- dimensionIndexFor(AxisType) - Static method in class org.anchoranalysis.spatial.axis.AxisTypeConverter
-
An index representing each dimension (0 for X, 1 for Y, 2 for Z)
- dimensions() - Method in class org.anchoranalysis.feature.energy.EnergyStack
-
The image-dimensions associated with the energy-stack.
- dimensions() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
- dimensions() - Method in class org.anchoranalysis.image.core.channel.Channel
- dimensions() - Method in class org.anchoranalysis.image.core.mask.Mask
- dimensions() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- dimensions() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- dimensions() - Method in class org.anchoranalysis.image.core.stack.Stack
- dimensions() - Method in class org.anchoranalysis.image.core.stack.TimeSequence
- dimensions() - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- dimensions() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
- dimensions() - Method in interface org.anchoranalysis.mpp.probmap.PointSampler
- dimensions() - Method in class org.anchoranalysis.mpp.probmap.ProbMapObjects
- dimensions() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
- dimensions() - Method in class org.anchoranalysis.mpp.segment.transformer.TransformationContext
- Dimensions - Class in org.anchoranalysis.image.core.dimensions
-
The dimensions of an image (in voxels), together with the image resolution.
- Dimensions(int, int, int) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions
-
Construct with an explicit extent and default resolution (1.0 for each dimension)
- Dimensions(Extent) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions
-
Construct with an explicit extent and default resolution (1.0 for each dimension)
- Dimensions(Extent, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions
- Dimensions(ReadableTuple3i) - Constructor for class org.anchoranalysis.image.core.dimensions.Dimensions
-
Construct with an explicit extent and default resolution (1.0 for each dimension)
- DimensionsChecker - Class in org.anchoranalysis.plugin.image.channel
- DimensionsCreator - Class in org.anchoranalysis.io.bioformats
- DimensionsCreator(IMetadata) - Constructor for class org.anchoranalysis.io.bioformats.DimensionsCreator
- dimensionsForSeries(int) - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
- dimensionsForSeries(int) - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
- dimensionsOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
- DimensionsProvider - Class in org.anchoranalysis.image.bean.provider
- DimensionsProvider() - Constructor for class org.anchoranalysis.image.bean.provider.DimensionsProvider
- dimensionsRequired() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
- DirectAssignMode<S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
-
Directly assigns a state for every optimisation step
- DirectAssignMode() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
- DirectAssignMode(ExtractScoreSize<S>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
- DirectionVector - Class in org.anchoranalysis.image.core.orientation
- DirectionVector() - Constructor for class org.anchoranalysis.image.core.orientation.DirectionVector
- DirectionVector(double, double, double) - Constructor for class org.anchoranalysis.image.core.orientation.DirectionVector
- DirectionVector(AxisType) - Constructor for class org.anchoranalysis.image.core.orientation.DirectionVector
-
Creates a direction aligned to a particular axis.
- DirectionVector(Tuple3d) - Constructor for class org.anchoranalysis.image.core.orientation.DirectionVector
- DirectionVectorBean - Class in org.anchoranalysis.image.bean.spatial.direction
-
A bean that creates a
DirectionVector - DirectionVectorBean() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.DirectionVectorBean
- DirectoryDepth - Class in org.anchoranalysis.plugin.io.bean.input.files.provider
-
Lists all directories to a certain depth
- DirectoryDepth() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
- DirectoryMatch - Class in org.anchoranalysis.io.manifest.finder.match
- DirectoryStructure - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
-
Reuses the directories between a path and its root to form the output - and also the filename.
- DirectoryStructure() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
- DirectoryWithPrefix - Class in org.anchoranalysis.io.output.path.prefixer
- DirectoryWithPrefix(Path) - Constructor for class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
- DirectoryWithPrefix(Path, String) - Constructor for class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
- dirtyInitialization() - Static method in class org.anchoranalysis.launcher.DirtyInitializer
-
Dirty initialisation work done that must be done every time we initialise an application that will use the Anchor platform
- DirtyInitializer - Class in org.anchoranalysis.launcher
-
Inelegant initialisation methods that should be done in the plugins themselves, when a proper framework exists for Initialising plugins
- disableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta
-
Assigns additional outputs to disable.
- DiscardOutliers - Class in org.anchoranalysis.plugin.image.bean.object.filter.dependent
-
Calculates features values for all objects, and discards any object less than
quantile - (minRatio * stdDev) - DiscardOutliers() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- DisplayStack - Class in org.anchoranalysis.image.core.stack
-
Stack that contains 1 or 3 channels so that we and display it as either or RGB unsigned 8-bit image
- distance(Mark, Mark) - Method in class org.anchoranalysis.mpp.bean.mark.MarkDistance
- distance(Mark, Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceAbstractPosition
- distance(Mark, Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceRadii
- distance(BoundingBox, BoundingBox, boolean) - Static method in class org.anchoranalysis.spatial.box.BoundingBoxDistance
- distance(Point2d) - Method in class org.anchoranalysis.spatial.point.Point2d
- distance(Point3d) - Method in class org.anchoranalysis.spatial.point.Point3d
-
Euclidean distance from this point to another
- distance(Point3d, Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- distance(Point3f) - Method in class org.anchoranalysis.spatial.point.Tuple3f
- distance(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3i
- distance(Point3i, Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- DistanceCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
- DistanceCondition(Optional<UnitValueDistance>, boolean, MessageLogger) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.DistanceCondition
- DistanceIndex - Class in org.anchoranalysis.image.core.outline.traverser.path
-
A distance, and the index the point came from
- DistanceIndex(int, int) - Constructor for class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
- distanceMax(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3i
-
The maximum distance across any axis
- distanceMaxToHeadTail(Point3i) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
-
The maximum-distance of a point to the closest contiguous-path
- DistancePhysical - Class in org.anchoranalysis.image.bean.unitvalue.distance
- DistancePhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
- distanceSquared(Point2d) - Method in class org.anchoranalysis.spatial.point.Point2d
- distanceSquared(Point3d) - Method in class org.anchoranalysis.spatial.point.Point3d
- distanceSquared(Point3d, Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
-
The square of the distance between two points taking account image-resolution.
- distanceSquared(Point3f) - Method in class org.anchoranalysis.spatial.point.Tuple3f
- distanceSquared(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3d
-
Square of Euclidean distance from this point to another
- distanceSquared(Point3i) - Method in class org.anchoranalysis.spatial.point.Point3i
- distanceSquared(Point3i, Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
-
The square of the distance between two points taking account image-resolution.
- distanceSquaredTo(Point3i) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult
- distanceSquaredZRelative(Point3d, Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- distanceSquaredZRelative(Point3i, Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- DistanceToContiguousPath - Class in org.anchoranalysis.image.core.outline.traverser.path
- DistanceTransform3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
-
Euclidian Distance Transform from ImageJ that works on 2D as well as 3D z-stacks.
- DistanceTransform3D() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
- DistanceTransformForEachObject3D - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
-
Like
DistanceTransform3Dbut applies the distance transform separately for each object in a collection. - DistanceTransformForEachObject3D() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
- DistanceVoxels - Class in org.anchoranalysis.image.bean.unitvalue.distance
- DistanceVoxels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
- DistanceVoxels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
- distanceZRelative(Point3d, Point3d) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- div(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
- div(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- div(AggIDCounter) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
- divide(int) - Method in class org.anchoranalysis.spatial.Extent
- Divide<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
- Divide() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
- divideBy(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- divideBy(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- divideBy(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- DivideByConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
- DivideByConstant() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.DivideByConstant
- divideByZeroReplace(double, double, double) - Static method in class org.anchoranalysis.math.arithmetic.DoubleUtilities
-
Replaces a value with a constant if the divider is 0
- Divider - Class in org.anchoranalysis.experiment.log
-
Creates a line of text that span a certain width with a repeated character, optionally containing a label.
- Divider() - Constructor for class org.anchoranalysis.experiment.log.Divider
-
A banner using dashes.
- Divider(char) - Constructor for class org.anchoranalysis.experiment.log.Divider
-
A banner using a particular repeated character.
- DO_NOT_CHANGE_EXISTING - org.anchoranalysis.image.core.channel.convert.ConversionPolicy
- doDuplicate(PointListBase) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
- doesClassInheritFromAny(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.task.InputTypesExpected
-
Does the childclass inherit from any one of expected input-types
- doesPathExist(String) - Method in class org.anchoranalysis.test.TestLoader
-
Does a resource exist with a particular folderPath + fileName
- doesPathExist(String, String) - Method in class org.anchoranalysis.test.TestLoader
-
Does a resource exist with a particular folderPath + fileName
- doFind(Manifest) - Method in interface org.anchoranalysis.io.manifest.finder.Finder
- doFind(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderExperimentFileDirectories
- doFind(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
- doFind(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleFile
- doInitFor(Object, Object, Object, Logger) - Method in interface org.anchoranalysis.bean.initializable.property.PropertyDefiner
- doInitFor(Object, Object, Object, Logger) - Method in class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
- doJobOnInput(InputBound<AnnotationWithStrategy<S>, AggregateSharedState>) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
- doJobOnInput(InputBound<NamedChannelsInput, SharedStateSelectedSlice>) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
- doJobOnInput(InputBound<NamedChannelsInput, S>) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
- doJobOnInput(InputBound<ProvidesStackInput, GroupedSharedState<S, T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
- doJobOnInput(InputBound<ProvidesStackInput, SharedStateFilteredImageOutput<T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
- doJobOnInput(InputBound<FileInput, CSVWriter>) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- doJobOnInput(InputBound<MultiInput, NoSharedState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
- doJobOnInput(InputBound<MultiInput, NoSharedState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- doJobOnInput(InputBound<MultiInput, CSVWriter>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
- doJobOnInput(InputBound<MultiInput, ExperimentState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
- doJobOnInput(InputBound<AnnotationComparisonInput<ProvidesStackInput>, SharedState<T>>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- doJobOnInput(InputBound<StackSequenceInput, SharedStateSegmentInstance<T>>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
- doJobOnInput(InputBound<ManifestCouplingDefinition, NoSharedState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
- doJobOnInput(InputBound<FromCSVInput, FromCSVSharedState>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
- doJobOnInput(InputBound<S, NoSharedState>) - Method in class org.anchoranalysis.experiment.bean.task.HelloWorld
- doJobOnInput(InputBound<T, SharedStateExportFeatures<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
- doJobOnInput(InputBound<T, Summarizer<S>>) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
- doJobOnInput(InputBound<T, S>) - Method in class org.anchoranalysis.experiment.bean.task.Task
-
Performs the task on a particular input.
- doJobOnInput(InputBound<T, S>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
- doOperation(VoxelizedMarkMemo, Dimensions) - Method in class org.anchoranalysis.mpp.feature.bean.mark.PxlListOperationFromMark
- doSeedsIntersect() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- doSeedsIntersectWithContainingMask(ObjectMask) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- doStack(InputBound<NamedChannelsInput, NoSharedState>, NoSharedState, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- doStack(InputBound<NamedChannelsInput, NoSharedState>, OutputSequenceIndexed<Stack, String>, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
- doStack(InputBound<NamedChannelsInput, OutputSequenceIncrementing<Stack>>, NoSharedState, int, int, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- doStack(InputBound<NamedChannelsInput, S>, U, int, int, InputOutputContext) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
-
Processes one stack from a series.
- dot(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- DotProductOrientationToVector - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
- DotProductOrientationToVector() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.DotProductOrientationToVector
- doubleFromFloat(Point2f) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- doubleFromFloat(Point3f) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- doubleFromInt(Point2i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- doubleFromInt(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- DoubleRange() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble.DoubleRange
- DoubleUtilities - Class in org.anchoranalysis.math.arithmetic
-
Utilities for arithmetic operations involving type
double - downcast() - Method in class org.anchoranalysis.feature.bean.Feature
-
Downcasts the feature
- DrawLineAlongConvexHull - Class in org.anchoranalysis.plugin.imagej.bean.object.provider
-
Draws a lines between successive points on the convex-hull of an object.
- DrawLineAlongConvexHull() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.provider.DrawLineAlongConvexHull
- DrawObject - Class in org.anchoranalysis.overlay.bean
-
Draws an object-mask on a RGB-stack
- DrawObject() - Constructor for class org.anchoranalysis.overlay.bean.DrawObject
- DrawOverlay - Class in org.anchoranalysis.overlay.writer
-
Draws an overlay onto a RGB-stack, including precalculated overlays.
- DrawOverlay() - Constructor for class org.anchoranalysis.overlay.writer.DrawOverlay
- dropKey() - Method in exception org.anchoranalysis.feature.calculate.NamedFeatureCalculateException
-
Ignores the name in the exception
- dropZ() - Method in class org.anchoranalysis.spatial.point.Point3d
-
Creates a new point with identical x and y, but with z set to 0
- DualMarks - Interface in org.anchoranalysis.annotation.mark
-
Two mark-collections, one considered accepted and the other rejected.
- DualMarksAnnotation<T> - Class in org.anchoranalysis.annotation.mark
-
An annotation that consists of two sets of marks, accepted and rejected.
- DualMarksAnnotation() - Constructor for class org.anchoranalysis.annotation.mark.DualMarksAnnotation
- DualStack - Class in org.anchoranalysis.mpp.segment.optimization
-
Stores an
EnergyStacktogether with a background stack. - DualStack(EnergyStack) - Constructor for class org.anchoranalysis.mpp.segment.optimization.DualStack
-
Creates to infer a background from the energy-stack.
- DualStack(EnergyStack, DisplayStack) - Constructor for class org.anchoranalysis.mpp.segment.optimization.DualStack
- DualState<T> - Class in org.anchoranalysis.mpp.segment.optimization
-
Remembers the current state of type T and some best state (which was once set from the current state)
- DualState() - Constructor for class org.anchoranalysis.mpp.segment.optimization.DualState
- DualVoxelizedMarks - Class in org.anchoranalysis.plugin.mpp.segment.optimization
-
A transformation of one
VoxelizedMarksWithEnergyinto another - DualVoxelizedMarks(VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.DualVoxelizedMarks
- DualWriterOperationRecorder - Class in org.anchoranalysis.io.manifest.operationrecorder
-
Allows two
WriteOperationRecorderfunction together as if they are one - DualWriterOperationRecorder(WriteOperationRecorder, WriteOperationRecorder) - Constructor for class org.anchoranalysis.io.manifest.operationrecorder.DualWriterOperationRecorder
- duplicate() - Method in class org.anchoranalysis.core.color.RGBColor
- duplicate() - Method in class org.anchoranalysis.core.value.KeyValueParams
- duplicate() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
- duplicate() - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
- duplicate() - Method in class org.anchoranalysis.image.core.channel.Channel
- duplicate() - Method in class org.anchoranalysis.image.core.mask.Mask
- duplicate() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- duplicate() - Method in interface org.anchoranalysis.image.core.object.seed.Seed
- duplicate() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- duplicate() - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
- duplicate() - Method in class org.anchoranalysis.image.core.orientation.Orientation
- duplicate() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- duplicate() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
- duplicate() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
- duplicate() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
- duplicate() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
- duplicate() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
- duplicate() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- duplicate() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
- duplicate() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
-
Immutably creates entirely new duplicated features
- duplicate() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- duplicate() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
- duplicate() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
-
Creates a deep copy of the current object, including deep-copying the associated buffer.
- duplicate() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
-
Deep copy, including duplicating object-masks
- duplicate() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- duplicate() - Method in class org.anchoranalysis.image.voxel.Voxels
- duplicate() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
- duplicate() - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
- duplicate() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle
-
Deep copy the current object.
- duplicate() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
- duplicate() - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
- duplicate() - Method in class org.anchoranalysis.math.arithmetic.RunningSum
-
Deep-copy
- duplicate() - Method in class org.anchoranalysis.math.histogram.Histogram
- duplicate() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
- duplicate() - Method in class org.anchoranalysis.math.moment.ImageMoments
- duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.Bound
- duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
- duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
- duplicate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
- duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
- duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- duplicate() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
- duplicate() - Method in class org.anchoranalysis.mpp.mark.Mark
- duplicate() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- duplicate() - Method in class org.anchoranalysis.mpp.mark.points.PointList
- duplicate() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
- duplicate() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
- duplicate() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
- duplicate() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
- duplicate() - Method in class org.anchoranalysis.plot.AxisLimits
- duplicate() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
- Duplicate - Class in org.anchoranalysis.plugin.image.bean.channel.provider
- Duplicate - Class in org.anchoranalysis.plugin.image.bean.mask.provider
- Duplicate - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Duplicates (deep copy) an object-collection.
- Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Duplicate
- Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Duplicate
- Duplicate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Duplicate
- duplicateBean() - Method in class org.anchoranalysis.bean.AnchorBean
-
Creates a new bean that deep-copies every property value.
- duplicateBean() - Method in class org.anchoranalysis.bean.define.Define
- duplicateBean() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
- duplicateBean() - Method in class org.anchoranalysis.bean.StringList
-
Duplicate the bean
- duplicateBean() - Method in class org.anchoranalysis.bean.StringSet
-
Duplicate the bean
- duplicateChangeExtent(Extent) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- duplicateChangeName(String) - Method in class org.anchoranalysis.feature.bean.Feature
-
Duplicates the feature as per
AnchorBean.duplicateBean()but sets a particular custom-name - duplicateChangeResolution(Optional<Resolution>) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- duplicateChangeZ(int) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- duplicateChangeZ(int) - Method in class org.anchoranalysis.spatial.Extent
- duplicateChangeZ(int) - Method in class org.anchoranalysis.spatial.point.Point3i
- duplicateChangeZ(int) - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
- duplicateDeep() - Method in class org.anchoranalysis.image.core.stack.Stack
-
Performs a deep copy of the stack, so that all channels are duplicated.
- duplicateFlattenZ(int) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- duplicateForNewThread() - Method in interface org.anchoranalysis.image.feature.session.FeatureTableCalculator
-
Makes a copy of the feature-store for a new thread.
- duplicateForNewThread() - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
- duplicateForNewThread() - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
- duplicateFresh() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
- duplicateHelper(Feature<FeatureInput>) - Method in class org.anchoranalysis.feature.bean.Feature
- duplicateHelper(KernelPosNeg<T>) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
- duplicateHelper(ConicFitterBase) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
- duplicateShallow() - Method in class org.anchoranalysis.image.core.stack.Stack
-
Performs a shallow copy of the stack, so that all channels are reused.
- duplicateShallow() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
-
Shallow copy of objects
E
- EachObjectIndependently - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine
-
Simply selects features directly from the list, and objects directly from the list passed.
- EachObjectIndependently() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
- EagerEvaluationStore<T> - Class in org.anchoranalysis.core.identifier.provider.store
-
Evaluates items via their Getter as soon as they are added
- EagerEvaluationStore() - Constructor for class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
- eccentricity(double, double) - Static method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.FeatureMarkEccentricity
-
Calculates eccentricity given two axes
- EccentricityAxisAligned - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
- EccentricityAxisAligned() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.EccentricityAxisAligned
- eccentricityForEllipsoid(double[], Orientation) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.EccentricityAxisAligned
- eccentricityForEllipsoid(double[], Orientation) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.EccentricityGuessXYPlane
- eccentricityForEllipsoid(double[], Orientation) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.FeatureMarkEccentricity
-
Calculates eccentricity in 3D-case
- EccentricityGuessXYPlane - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
- EccentricityGuessXYPlane() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.EccentricityGuessXYPlane
- EdgeAdderParameters - Class in org.anchoranalysis.image.voxel.neighborhood
- EdgeAdderParameters(boolean) - Constructor for class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
- EdgeFilterIJ - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
- EdgeFilterIJ() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.EdgeFilterIJ
- edgesMaybeDuplicates() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
The edges in the graph, all of them, but with some edges possibly duplicated.
- edgesUnique() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
The edges in the graph, all of them, without any duplicates.
- effectiveBitsPerPixel(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
- effectiveBitsPerPixel(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
- effectiveBitsPerPixel(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
- EigenvalueAndVector - Class in org.anchoranalysis.math.moment
-
An eigen-value and its corresponding eigen-vector.
- EigenvalueAndVector(double, DoubleMatrix1D) - Constructor for class org.anchoranalysis.math.moment.EigenvalueAndVector
- eigenvalueNormalizedAsAxisLength() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
-
A normalization of an eigen-value to represent axis-length.
- eitherFunctionAndType(String, String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DescriptionMatch
- elementRange() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
- elementRange() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
- elementRange() - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
- elementRange() - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
- ElementSupplier<T> - Interface in org.anchoranalysis.io.output.writer
-
Creates or gets a element to output files together with a
ElementWriter. - elementwiseOperation(ReadableTuple3i, ReadableTuple3i, IntBinaryOperator) - Static method in class org.anchoranalysis.spatial.point.Point3i
-
Applies an operation to each element across two points
- ElementWriter<T> - Interface in org.anchoranalysis.io.output.writer
-
Writes an element (with or without an index) to the file system.
- ElementWriterSupplier<T> - Interface in org.anchoranalysis.io.output.writer
-
Creates or gets a element-writer to output files.
- Ellipse - Class in org.anchoranalysis.mpp.mark.conic
- Ellipse() - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipse
- Ellipse(Ellipse) - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipse
- EllipseBounds - Class in org.anchoranalysis.mpp.bean.mark.bounds
- EllipseBounds() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
- EllipseBounds(Bound) - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
- EllipseBounds(EllipseBounds) - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
- EllipseBoundsCheck - Class in org.anchoranalysis.plugin.mpp.bean.check
- EllipseBoundsCheck() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.EllipseBoundsCheck
- EllipseBoundsWithoutRotation - Class in org.anchoranalysis.mpp.bean.mark.bounds
- EllipseBoundsWithoutRotation() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
- EllipseBoundsWithoutRotation(Bound) - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
- EllipseBoundsWithoutRotation(EllipseBoundsWithoutRotation) - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
- EllipseStandardFormConverter - Class in org.anchoranalysis.plugin.points.bean.fitter
- EllipseStandardFormConverter(DoubleMatrix1D) - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
- Ellipsoid - Class in org.anchoranalysis.mpp.mark.conic
- Ellipsoid() - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- Ellipsoid(Ellipsoid) - Constructor for class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- EllipsoidAxisRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
- EllipsoidAxisRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.EllipsoidAxisRatio
- EllipsoidBase - Class in org.anchoranalysis.plugin.points.bean.feature.object.conic
- EllipsoidBase() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
- EllipsoidFactory - Class in org.anchoranalysis.plugin.points.calculate.ellipsoid
- EllipsoidFitHelper - Class in org.anchoranalysis.plugin.points.bean.fitter
- Ellipsoidicity - Class in org.anchoranalysis.plugin.points.bean.feature.object.conic
- Ellipsoidicity() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.object.conic.Ellipsoidicity
- EllipsoidMaxAreaIntersectingPlane - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
- EllipsoidMaxAreaIntersectingPlane() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.EllipsoidMaxAreaIntersectingPlane
- EllipsoidOrientationRadii - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
- EllipsoidOrientationRadii() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
- EllipsoidUtilities - Class in org.anchoranalysis.mpp.mark.conic
- Ellipticity - Class in org.anchoranalysis.plugin.points.bean.feature.object.conic
- Ellipticity() - Constructor for class org.anchoranalysis.plugin.points.bean.feature.object.conic.Ellipticity
- empty() - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
-
Creates an empty list of features
- empty() - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a newly created object-collection that is empty
- Empty - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Creates an empty object-collection.
- Empty() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Empty
- EmptyHistogramConstant - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Specifies a constant if a histogram is empty, otherwise delegates to another {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
- EmptyHistogramConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
- enableAdditionalOutputs(MultiLevelOutputEnabled) - Method in class org.anchoranalysis.io.output.recorded.OutputEnabledDelta
-
Assigns additional outputs to enable.
- encodeConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
- EncodedIntBuffer - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
- EncodedIntBuffer(UnsignedIntBuffer, WatershedEncoding) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
- encodeDirection(int, int, int) - Method in interface org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodeDirection
- encodeDirection(int, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
- EncodeDirection - Interface in org.anchoranalysis.plugin.image.segment.watershed.encoding
- EncodedVoxels - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
- EncodedVoxels(Voxels<UnsignedIntBuffer>) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- ENCODING - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- end() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput
- end() - Method in class org.anchoranalysis.mpp.feature.bean.mark.CheckMark
- end() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
- end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
- end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
- end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
- end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
- end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
- end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
- end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
- end() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
- end() - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
- endSeries(NoSharedState, NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- endSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
- endSeries(OutputSequenceIncrementing<Stack>, NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- endSeries(S, U, InputOutputContext) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
-
Ends processing of a series.
- ENERGY_STACK - Static variable in class org.anchoranalysis.image.experiment.identifiers.StackIdentifiers
- EnergyPair - Class in org.anchoranalysis.mpp.feature.energy
- EnergyPair(IdentifiablePair<Mark>, EnergyTotal) - Constructor for class org.anchoranalysis.mpp.feature.energy.EnergyPair
- EnergySavedAll - Class in org.anchoranalysis.mpp.feature.energy.saved
- EnergySavedAll() - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
- EnergySavedInd - Class in org.anchoranalysis.mpp.feature.energy.saved
- EnergySavedInd() - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- EnergySavedPairs - Class in org.anchoranalysis.mpp.feature.energy.saved
- EnergySavedPairs(AddCriteria<EnergyPair>) - Constructor for class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
- EnergyScheme - Class in org.anchoranalysis.mpp.feature.energy.scheme
-
The energy for a feature-list as factorized into different cliques.
- EnergyScheme(FeatureList<FeatureInputSingleMemo>, FeatureList<FeatureInputPairMemo>, FeatureList<FeatureInputAllMemo>, RegionMap, AddCriteriaPair) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
- EnergyScheme(FeatureList<FeatureInputSingleMemo>, FeatureList<FeatureInputPairMemo>, FeatureList<FeatureInputAllMemo>, RegionMap, AddCriteriaPair, Optional<KeyValueParamsProvider>, List<NamedBean<Feature<FeatureInputStack>>>) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
- EnergySchemeCreator - Class in org.anchoranalysis.mpp.feature.bean.energy.scheme
- EnergySchemeCreator() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreator
- EnergySchemeCreatorByElement - Class in org.anchoranalysis.mpp.feature.bean.energy.scheme
- EnergySchemeCreatorByElement() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- EnergySchemeSet - Class in org.anchoranalysis.mpp.feature.energy.scheme
-
A set of EnergySchemes each with a name.
- EnergySchemeSet(SharedFeatureMulti) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
- EnergySchemeWithSharedFeatures - Class in org.anchoranalysis.mpp.feature.energy.scheme
- EnergySchemeWithSharedFeatures(EnergyScheme, SharedFeatureMulti, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
- energyStack() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
-
The specified energy stack.
- energyStack() - Static method in class org.anchoranalysis.test.feature.plugins.objects.CircleObjectFixture
- EnergyStack - Class in org.anchoranalysis.feature.energy
-
An energy-stack with associated
KeyValueParams. - EnergyStack(EnergyStackWithoutParams) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
- EnergyStack(EnergyStackWithoutParams, KeyValueParams) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
- EnergyStack(Channel) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
- EnergyStack(Dimensions) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
- EnergyStack(Stack) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
- EnergyStack(Stack, KeyValueParams) - Constructor for class org.anchoranalysis.feature.energy.EnergyStack
- EnergyStackWithoutParams - Class in org.anchoranalysis.feature.energy
-
A stack of channels used as context to calculate features (or calculating energy more broadly).
- EnergyStackWithoutParams(Channel) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
-
Create a energy-stack comprised of a single channel
- EnergyStackWithoutParams(Dimensions) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
-
Create a energy-stack with no channels - but with dimensions associated
- EnergyStackWithoutParams(Stack) - Constructor for class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
-
Create a energy-stack comprised of all channels from a stack
- EnergyStackWriter - Class in org.anchoranalysis.mpp.io.output
-
Writes an energy-stack.
- EnergyStackWriter(EnergyStack, Outputter) - Constructor for class org.anchoranalysis.mpp.io.output.EnergyStackWriter
- EnergyTotal - Class in org.anchoranalysis.feature.energy
- EnergyTotal() - Constructor for class org.anchoranalysis.feature.energy.EnergyTotal
- EnergyTotal(double) - Constructor for class org.anchoranalysis.feature.energy.EnergyTotal
- EnsureRegExMatch - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
-
Rejects files that fail to match a particular regular-expression
- EnsureRegExMatch() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.EnsureRegExMatch
- entrySet() - Method in class org.anchoranalysis.core.identifier.name.MapCreate
- entrySet() - Method in class org.anchoranalysis.image.experiment.label.FileLabelMap
- equalMask(BoundingBox, int) - Method in class org.anchoranalysis.image.core.channel.Channel
- equals(Object) - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
- equals(Object) - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
- equals(Object) - Method in class org.anchoranalysis.annotation.io.image.findable.Found
- equals(Object) - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
- equals(Object) - Method in interface org.anchoranalysis.bean.GenerateUniqueParameterization
- equals(Object) - Method in class org.anchoranalysis.bean.shared.path.RootPath
- equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
- equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
- equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
- equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
- equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
- equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
- equals(Object) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- equals(Object) - Method in class org.anchoranalysis.core.color.RGBColor
- equals(Object) - Method in class org.anchoranalysis.core.concurrency.WithPriority
- equals(Object) - Method in class org.anchoranalysis.core.graph.TypedEdge
- equals(Object) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
- equals(Object) - Method in class org.anchoranalysis.core.index.Indexable
- equals(Object) - Method in class org.anchoranalysis.core.log.CommonContext
- equals(Object) - Method in class org.anchoranalysis.core.system.path.SplitPath
- equals(Object) - Method in class org.anchoranalysis.core.value.TypedValue
- equals(Object) - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
- equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
- equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculation
- equals(Object) - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculationMap
- equals(Object) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
- equals(Object) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
- equals(Object) - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
- equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
- equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputNull
- equals(Object) - Method in class org.anchoranalysis.feature.input.FeatureInputResults
- equals(Object) - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
- equals(Object) - Method in class org.anchoranalysis.feature.io.name.CombinedName
- equals(Object) - Method in interface org.anchoranalysis.feature.io.name.MultiName
-
If another name is equal to the current name
- equals(Object) - Method in class org.anchoranalysis.feature.io.name.SimpleName
- equals(Object) - Method in class org.anchoranalysis.feature.results.ResultsVector
- equals(Object) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
- equals(Object) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
- equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel
- equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
- equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
- equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
- equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
- equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
- equals(Object) - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
- equals(Object) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- equals(Object) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- equals(Object) - Method in class org.anchoranalysis.image.core.mask.Mask
- equals(Object) - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
- equals(Object) - Method in class org.anchoranalysis.image.core.object.MatchedObject
- equals(Object) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- equals(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation
- equals(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- equals(Object) - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
- equals(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
- equals(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
- equals(Object) - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
- equals(Object) - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
- equals(Object) - Method in class org.anchoranalysis.image.core.stack.Stack
- equals(Object) - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
- equals(Object) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
- equals(Object) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
- equals(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
- equals(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
- equals(Object) - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
- equals(Object) - Method in class org.anchoranalysis.image.feature.stack.FeatureInputStack
- equals(Object) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
- equals(Object) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
- equals(Object) - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
- equals(Object) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
- equals(Object) - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
- equals(Object) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
-
Checks if two collections are equal in a shallow way
- equals(Object) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
- equals(Object) - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
- equals(Object) - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
- equals(Object) - Method in class org.anchoranalysis.io.manifest.file.FileType
- equals(Object) - Method in class org.anchoranalysis.io.manifest.ManifestDescription
- equals(Object) - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
- equals(Object) - Method in class org.anchoranalysis.io.output.outputter.Outputter
- equals(Object) - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
- equals(Object) - Method in class org.anchoranalysis.launcher.config.HelpConfig
- equals(Object) - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
- equals(Object) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
- equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
- equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- equals(Object) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
- equals(Object) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
- equals(Object) - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
- equals(Object) - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
- equals(Object) - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
- equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
- equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
- equals(Object) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
- equals(Object) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
- equals(Object) - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
- equals(Object) - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
- equals(Object) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
- equals(Object) - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
- equals(Object) - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
- equals(Object) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
- equals(Object) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
- equals(Object) - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
- equals(Object) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- equals(Object) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
- equals(Object) - Method in class org.anchoranalysis.overlay.IndexableOverlays
- equals(Object) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
- equals(Object) - Method in class org.anchoranalysis.overlay.Overlay
- equals(Object) - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
- equals(Object) - Method in class org.anchoranalysis.plot.AxisLimits
- equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
- equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
- equals(Object) - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
- equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
- equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
- equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
- equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
- equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
- equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
- equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
- equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
- equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
- equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
- equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
- equals(Object) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
- equals(Object) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
- equals(Object) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
- equals(Object) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
- equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
- equals(Object) - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
- equals(Object) - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
- equals(Object) - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
- equals(Object) - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
- equals(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
- equals(Object) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Specific
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
- equals(Object) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
- equals(Object) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
- equals(Object) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
- equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
- equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
- equals(Object) - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
- equals(Object) - Method in class org.anchoranalysis.spatial.box.BoundingBox
- equals(Object) - Method in class org.anchoranalysis.spatial.Extent
- equals(Object) - Method in class org.anchoranalysis.spatial.point.Point2d
- equals(Object) - Method in class org.anchoranalysis.spatial.point.Point2f
- equals(Object) - Method in class org.anchoranalysis.spatial.point.Point2i
- equals(Object) - Method in class org.anchoranalysis.spatial.point.Point3d
- equals(Object) - Method in class org.anchoranalysis.spatial.point.Point3f
- equals(Object) - Method in class org.anchoranalysis.spatial.point.Point3i
- equals(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- equals(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3f
- equals(Object) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- equals(Object) - Method in class org.anchoranalysis.spatial.point.Vector3d
- equals(Object) - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
- equals(Object...) - Method in class org.anchoranalysis.feature.results.ResultsVector
- equals(Dimensions, boolean) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
-
Checks equality betwen this object and another
Dimensions, maybe not comparing image-resolution. - equalsDeep(Channel, boolean) - Method in class org.anchoranalysis.image.core.channel.Channel
-
Are the two channels equal using a deep voxel by voxel comparison?
- equalsDeep(Seed) - Method in interface org.anchoranalysis.image.core.object.seed.Seed
- equalsDeep(Seed) - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
- equalsDeep(Stack, boolean) - Method in class org.anchoranalysis.image.core.stack.Stack
-
Are the two stack equal using a deep voxel by voxel comparison of each channel?
- equalsDeep(BoundedVoxels<?>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
- equalsDeep(ObjectCollection) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
-
Checks if two collections are equal in a deeper way
- equalsDeep(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- equalsDeep(Voxels<?>) - Method in class org.anchoranalysis.image.voxel.Voxels
-
Are the voxels identical to another voxels (deep equals)?
- equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.Mark
- equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
- equalsDeep(Mark) - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
- equalsDeep(MarkCollection) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- equalsID(Object) - Method in class org.anchoranalysis.mpp.mark.Mark
- equalsIgnoreZ(Object) - Method in class org.anchoranalysis.spatial.Extent
-
Checks for equality with another extent ignoring any differences in the Z dimension
- equalsPrecision(double, Object...) - Method in class org.anchoranalysis.feature.results.ResultsVector
- EqualTo - Class in org.anchoranalysis.math.relation
- EqualTo() - Constructor for class org.anchoranalysis.math.relation.EqualTo
- EqualToBean - Class in org.anchoranalysis.bean.shared.relation
- EqualToBean() - Constructor for class org.anchoranalysis.bean.shared.relation.EqualToBean
- equalToPrimitive(Voxels<UnsignedByteBuffer>, byte, ScalarThreeDimensionalConsumer) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo
-
Iterates through all points with a specific voxel intensity-value, passing coordinates as primitive types.
- equalToPrimitiveSlice(Voxels<UnsignedByteBuffer>, int, byte, ScalarThreeDimensionalConsumer) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo
- equalToReusePoint(Voxels<UnsignedByteBuffer>, byte, Consumer<Point3i>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo
-
Iterates all points with a specific voxel intensity-value, reusing the
Point3iin each iteration. - erode(BinaryVoxels<UnsignedByteBuffer>, boolean, int, Optional<Voxels<UnsignedByteBuffer>>, int, boolean, Optional<AcceptIterationConditon>) - Static method in class org.anchoranalysis.image.voxel.object.morphological.MorphologicalErosion
-
Performs a morphological erosion by dilating an inverted version of the object
- Erode - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
-
Performs an erosion morphological operation on a binary-image
- Erode - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
-
Erodes each object in the collection, growing bounding-boxes as necessary in relevant dimensions.
- Erode - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
- Erode() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
- Erode() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
- Erode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
- ErosionKernel3 - Class in org.anchoranalysis.image.voxel.kernel.dilateerode
-
Erosion with a 3x3 or 3x3x3 kernel
- ErosionKernel3(BinaryValuesByte, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.dilateerode.ErosionKernel3
- errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
- errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
- errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
- errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
- errorMessageIfTooFewPixels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
- ErrorNode - Class in org.anchoranalysis.mpp.proposer.error
- ErrorNode() - Constructor for class org.anchoranalysis.mpp.proposer.error.ErrorNode
- ErrorNodeException - Exception in org.anchoranalysis.mpp.proposer.error
- ErrorNodeException(Exception) - Constructor for exception org.anchoranalysis.mpp.proposer.error.ErrorNodeException
- ErrorNodeException(String) - Constructor for exception org.anchoranalysis.mpp.proposer.error.ErrorNodeException
- ErrorNodeImpl - Class in org.anchoranalysis.mpp.proposer.error
- ErrorNodeNull - Class in org.anchoranalysis.mpp.proposer.error
-
Singleton that does nothing with errors
- errorReporter() - Method in class org.anchoranalysis.core.log.Logger
-
Where errors are reported to
- ErrorReporter - Interface in org.anchoranalysis.core.log.error
- ErrorReporterForTask - Class in org.anchoranalysis.experiment.task
-
An error-reporter that replaces particular errors/exceptions with user-friendly messages.
- ErrorReporterForTask(MessageLogger) - Constructor for class org.anchoranalysis.experiment.task.ErrorReporterForTask
- ErrorReporterIntoLog - Class in org.anchoranalysis.core.log.error
-
Records errors, by writing them into a logger.
- ErrorReporterIntoLog(MessageLogger) - Constructor for class org.anchoranalysis.core.log.error.ErrorReporterIntoLog
- evalPointInside(Point3i) - Method in class org.anchoranalysis.mpp.mark.Mark
- exchange(int, EnergyTotal) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- exchange(int, Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- exchange(int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- exchange(int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
- exchange(int, VoxelizedMarkMemo, EnergyStack) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- exchange(EnergySavedInd, int, VoxelizedMarkMemo, EnergyStackWithoutParams, EnergySchemeWithSharedFeatures) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
- exchange(MemoCollection, int, VoxelizedMarkMemo, EnergyStack) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
- exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- exchange(MemoForIndex, VoxelizedMarkMemo, int, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.set.UpdatableMarkSet
- exchangeOnUpdatablePairList(ListUpdatableMarkSetCollection, Mark, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- Exclude<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Excludes all inputs that match a regular expression
- Exclude() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Exclude
- excuteOrWait(CheckedFunction<T, S, ConcurrentModelException>) - Method in class org.anchoranalysis.core.concurrency.ConcurrentModelPool
-
Execute on the next available model (or wait until one becomes available)
- execExperiment(String, String) - Static method in class org.anchoranalysis.test.experiment.launcher.UnitTestCompareUtilities
-
As we use a common format for storing our tests for the different modules.
- execExperimentInTemporary(String, String, boolean, TemporaryFolder) - Static method in class org.anchoranalysis.test.experiment.launcher.UnitTestCompareUtilities
-
As we use a common format for storing our tests for the different modules.
- execute() - Method in interface org.anchoranalysis.io.output.writer.WriterExecuteBeforeEveryOperation
-
Is called before every operation
- execute() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
-
Execute the algorithm.
- execute(FeatureInputPairObjects) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
- execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
- execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
- execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
- execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
- execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
- execute(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
- execute(FeatureInputSingleObject, Integer) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
- execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
- execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
- execute(FeatureInputStack) - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
- execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
- execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
-
The job processor is expected to remove items from the inputs-list as they are consumed so as to allow garbage-collection of these items before all jobs are processed (as the list might be quite large).
- execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
- execute(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.SequentialProcessor
- execute(FeatureInputAllMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
- execute(FeatureInputAllMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
- execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
- execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
- execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
- execute(FeatureInputPairMemo) - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
- execute(T) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
-
This performs the actual calculation when needed.
- execute(T) - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
- execute(T, U) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
- executeAndAssertCount(int, int, CheckedRunnable<OperationFailedException>) - Static method in class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculationFixture
-
Executes an operation, and afterwards asserts an expected number of times certain internal methods are called on a mock-calculation.
- executeEachWithMonitor(String, List<T>) - Method in class org.anchoranalysis.experiment.task.processor.MonitoredSequentialExecutor
-
Executes code for each element of inputs in serial, providing log-reports as to how many are finished, remain etc.
- executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.experiment.bean.Experiment
- executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
-
Executes the experiment for given arguments.
- executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- executeExperiment(ExperimentExecutionArguments) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- executeExperiment(ExperimentExecutionArguments, boolean, MessageLogger) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
-
Executes an experiment after finding a single experiment XML file, and reading the experiment from this file
- executeExperimentWithParams(ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
- executeExperimentWithParams(ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
-
Executes the experiment for parameters.
- executeJob(ParametersUnbound<T, S>) - Method in class org.anchoranalysis.experiment.bean.task.Task
-
Runs the task on one particular input (a job).
- executeLogStats(Outputter, List<T>, ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
-
Executes the tasks, gathers statistics, and logs them
- executePhase() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
-
Execute a single phase of the algorithm.
- executingTasks() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- exists() - Method in interface org.anchoranalysis.io.manifest.finder.Finder
- exists() - Method in class org.anchoranalysis.io.manifest.finder.FinderExperimentFileDirectories
- exists() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
- exists() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleFile
- existsWith(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection
-
Does this bounding box intersect with another?
- existsWithAny(List<BoundingBox>) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection
-
Does this bounding box intersection with any of the others in the list?
- Experiment - Class in org.anchoranalysis.experiment.bean
- Experiment() - Constructor for class org.anchoranalysis.experiment.bean.Experiment
- ExperimentExecutionArguments - Class in org.anchoranalysis.experiment
- ExperimentExecutionArguments() - Constructor for class org.anchoranalysis.experiment.ExperimentExecutionArguments
- ExperimentExecutionArguments(Path) - Constructor for class org.anchoranalysis.experiment.ExperimentExecutionArguments
- ExperimentExecutionException - Exception in org.anchoranalysis.experiment
-
An exception that occurs when an experiment is executed.
- ExperimentExecutionException(String) - Constructor for exception org.anchoranalysis.experiment.ExperimentExecutionException
- ExperimentExecutionException(String, Throwable) - Constructor for exception org.anchoranalysis.experiment.ExperimentExecutionException
-
A string message displayed to the user as well as a stack-trace of the cause
- ExperimentExecutionException(Throwable) - Constructor for exception org.anchoranalysis.experiment.ExperimentExecutionException
- ExperimentExecutor - Class in org.anchoranalysis.launcher.executor
-
Determines where the files passed the ExperimentExecutor are loaded from.
- ExperimentExecutorFactory - Class in org.anchoranalysis.launcher.executor
- ExperimentFactory - Class in org.anchoranalysis.launcher.executor.selectparam.experiment
-
SelectParam<Path>factory for experiments. - ExperimentIdentifier - Class in org.anchoranalysis.experiment.bean.identifier
- ExperimentIdentifier() - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifier
- ExperimentIdentifierAuto - Class in org.anchoranalysis.experiment.bean.identifier
-
Automatically populates a experiment-name and version number
- ExperimentIdentifierAuto() - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
- ExperimentIdentifierConstant - Class in org.anchoranalysis.experiment.bean.identifier
-
Defines constants for name and version of an experiment
- ExperimentIdentifierConstant() - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
- ExperimentIdentifierConstant(String, String) - Constructor for class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
- ExperimentLauncherFromShell - Class in org.anchoranalysis.test.experiment.launcher
-
Launches an experiment by calling the application 'anchor' via the shell.
- ExperimentLauncherFromShell(TestLoader) - Constructor for class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell
- ExperimentResultsExperimentStructure - Class in org.anchoranalysis.plugin.quick.bean.structure
-
Finds some files produced in a previous experiment assuming a certain structure
- ExperimentResultsExperimentStructure() - Constructor for class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
- experimentSelectParam(CommandLine, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory
-
Can point to either: a path ending in .xml, assumed to BeanXML for an experiment nothing, then default experiment is used
- ExperimentState - Interface in org.anchoranalysis.mpp.segment.bean
- ExperimentStructure - Class in org.anchoranalysis.plugin.quick.bean.structure
-
A file path prefixer that combines a prefix with an experimentType
- ExperimentStructure() - Constructor for class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
- ExportFeatureResultsAdder - Interface in org.anchoranalysis.plugin.image.task.feature
-
Adds results (a row in a feature-table) for export-features
- ExportFeatures<T extends InputFromManager,S,U extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature
-
Calculates features and exports them as a CSV
- ExportFeatures() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
- ExportImageHistograms - Class in org.anchoranalysis.plugin.image.task.bean.grouped.histogram
-
Exports a histogram of voxel intensities as a CSV file for each channel of an image.
- ExportImageHistograms() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
- ExportObjectsAsCroppedImages - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects
-
Exports a cropped image for each object-mask showing its context within an image
- ExportObjectsAsCroppedImages() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- ExportObjectsBase<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects
- ExportObjectsBase() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
- ExportObjectsFromCSV - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects
-
Given a CSV with a point representing an object-mask, the object-masks are extracted from a segmentation
- ExportObjectsFromCSV() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
- ExportReportFeatures - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
- ExportReportFeatures() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
- ExportReportFeaturesFromManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
- ExportReportFeaturesFromManifest() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
- ExtendInZ - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice
-
Creates a 3D version of an object by replicating each input-object across the z-dimension to meet (3D) dimensions.
- ExtendInZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZ
- ExtendInZWithinContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice
-
Extends an object (2D/3D) as much as it can within the z-slices of a containing object
- ExtendInZWithinContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.ExtendInZWithinContainer
- extendWith(int) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2
-
Switches to extend constant-value out-of-bounds strategy
- ExtensionCount - Class in org.anchoranalysis.plugin.io.bean.summarizer.path
-
Remembers each unique extension, and associated count
- ExtensionCount() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.ExtensionCount
- extensionSuffix(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
- extensionSuffix(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.SerializedGenerator
-
Appended to the standard "serialized" extension, to form the complete extension
- extensionSuffix(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.XStreamGenerator
- extent - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3Extent
- extent() - Method in class org.anchoranalysis.feature.energy.EnergyStack
- extent() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
- extent() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
- extent() - Method in class org.anchoranalysis.image.core.channel.Channel
- extent() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
-
The width and height and depth of the image i.e.
- extent() - Method in class org.anchoranalysis.image.core.mask.Mask
- extent() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- extent() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- extent() - Method in class org.anchoranalysis.image.core.stack.Stack
- extent() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- extent() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
- extent() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
- extent() - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
- extent() - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
- extent() - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
- extent() - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
- extent() - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
- extent() - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
- extent() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- extent() - Method in class org.anchoranalysis.image.voxel.Voxels
- extent() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- extent() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- extent() - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
Dimensions in pixels needed to represent the bounding box
- Extent<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
-
Width/height/depth of energy-stack in pixels depending on axis
- Extent - Class in org.anchoranalysis.spatial
-
Width, height etc.
- Extent() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Extent
- Extent(int, int) - Constructor for class org.anchoranalysis.spatial.Extent
-
Creates with with only x and y dimensions (z dimension is assumed to be 1)
- Extent(int, int, int) - Constructor for class org.anchoranalysis.spatial.Extent
-
Creates with x and y and z dimensions
- ExtentMatchHelper - Class in org.anchoranalysis.image.voxel
- extract() - Method in class org.anchoranalysis.image.core.channel.Channel
- extract() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- extract() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
Extracts value from voxels using global coordinates
- extract() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- extract() - Method in class org.anchoranalysis.image.voxel.Voxels
-
Methods to read/copy/duplicate the voxel-values
- extract() - Method in class org.anchoranalysis.image.voxel.VoxelsAsFloat
- extract() - Method in class org.anchoranalysis.image.voxel.VoxelsAsInt
- extract() - Method in class org.anchoranalysis.image.voxel.VoxelsAsShort
- extract() - Method in class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
- extract() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- extract(S) - Method in class org.anchoranalysis.bean.initializable.property.ExtractFromParam
- ExtractCenterSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
-
Extracts the slice at the center (rounding down) of the range of z-stacks.
- ExtractCenterSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractCenterSlice
- extractChannel(String, boolean) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
- extractChannel(String, boolean, int) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
- extractChannel(Stack, boolean, int) - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
- ExtractDescriptiveName<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
- ExtractDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractDescriptiveName
- ExtractDescriptiveNameAndPath<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
- ExtractDescriptiveNameAndPath() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractDescriptiveNameAndPath
- extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractDescriptiveName
- extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractDescriptiveNameAndPath
- extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractPath
- extractFrom(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
- ExtractFromParam<S,T> - Class in org.anchoranalysis.bean.initializable.property
-
Extracts on type of parameter from another
- ExtractFromParam(Class<?>, Function<S, T>) - Constructor for class org.anchoranalysis.bean.initializable.property.ExtractFromParam
-
Constructor
- ExtractFromParam(Class<?>, Function<S, T>, Class<?>) - Constructor for class org.anchoranalysis.bean.initializable.property.ExtractFromParam
-
Constructor
- extractFromVoxelized(VoxelizedMark) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
- extractFromVoxelized(VoxelizedMark) - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
- extractFromVoxelized(VoxelizedMark) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
- extractKey(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.BitDepth
- extractKey(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
- extractKey(NamedChannelsInput) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannelsSimple
- extractObjectForSummary(T) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
- extractObjectForSummary(T) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
- extractParamsAsDouble(KeyValueParams, String) - Static method in class org.anchoranalysis.plugin.image.feature.bean.score.FromParamsBase
- ExtractPath<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
- ExtractPath() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.ExtractPath
- extractScore(VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromVoxelizedMarksWithEnergy
- extractScore(DualVoxelizedMarks) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromDualVoxelizedMarks
- extractScore(ToPixelized<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.ToPixelizedExtracter
- extractScore(T) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.ExtractScoreSize
- ExtractScoreSize<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization
- ExtractScoreSize() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.ExtractScoreSize
- extractScoreSizeReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
- extractScoreSizeReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
- extractScoreSizeReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- extractScoreSizeState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
- extractScoreSizeState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
- extractScoreSizeState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- extractSize(VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromVoxelizedMarksWithEnergy
- extractSize(DualVoxelizedMarks) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromDualVoxelizedMarks
- extractSize(ToPixelized<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.ToPixelizedExtracter
- extractSize(T) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.ExtractScoreSize
- extractSlice(int) - Method in class org.anchoranalysis.feature.energy.EnergyStack
- extractSlice(int) - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
- extractSlice(int) - Method in class org.anchoranalysis.image.core.channel.Channel
-
Creates a new channel contain only of a particular slice (reusing the voxel buffers)
- extractSlice(int) - Method in class org.anchoranalysis.image.core.mask.Mask
- extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.Stack
- extractSlice(int) - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
- extractSlice(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- extractSlice(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
Extracts a particular slice.
- extractSlice(int, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Extracts one particular slice as an object-mask
- ExtractSlice - Class in org.anchoranalysis.plugin.image.task.bean.slice
-
Reduces a z-stack to a single-slice by taking the optima of a feature calculated for each slice
- ExtractSlice() - Constructor for class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
- ExtractSliceRange - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
-
Extracts slices from
sliceStart(inclusive) tosliceEnd(inclusive) - ExtractSliceRange() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
- extractStack(ProvidesStackInput, StackProvider, InputOutputContext) - Static method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorRepeated
- extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
- extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxExtentAlongAxis
- extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMaximumAlongAxis
- extractTupleForBoundingBox(BoundingBox) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxMinimumAlongAxis
- extractUpToThreeChannels() - Method in class org.anchoranalysis.image.core.stack.Stack
- extractValuesFromLeft(long) - Method in class org.anchoranalysis.math.histogram.Histogram
- extractValuesFromRight(long) - Method in class org.anchoranalysis.math.histogram.Histogram
- ExtractWeightFromMark - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
- ExtractWeightFromMark() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ExtractWeightFromMark
F
- factory() - Method in class org.anchoranalysis.image.voxel.Voxels
- factoryParamsOnly() - Static method in class org.anchoranalysis.feature.list.NamedFeatureStoreFactory
- FailureOnlyMessageLogger - Class in org.anchoranalysis.experiment.log
-
Writes text to a file, but only if
FailureOnlyMessageLogger.close(boolean)is called withsuccessful==true. - FailureOnlyMessageLogger(String, OutputterChecked, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
- Feature<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean
-
Feature that calculates a result (double) for some parameters
- Feature() - Constructor for class org.anchoranalysis.feature.bean.Feature
- Feature(PropertyInitializer<FeatureInitParams>) - Constructor for class org.anchoranalysis.feature.bean.Feature
- FeatureAllMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element
- FeatureAllMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureAllMemo
- FeatureAsIndividualProportionate - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
-
Calculates each feature individually, and combines them using the ratios between itemProportionate as weights
- FeatureAsIndividualProportionate() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeatureAsIndividualProportionate
- FeatureCalculation<S,T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate
-
Caches the result of a feature, until
FeatureCalculation.invalidate()is called. - FeatureCalculation() - Constructor for class org.anchoranalysis.feature.calculate.FeatureCalculation
- FeatureCalculationException - Exception in org.anchoranalysis.feature.calculate
- FeatureCalculationException(String) - Constructor for exception org.anchoranalysis.feature.calculate.FeatureCalculationException
- FeatureCalculationException(String, Throwable) - Constructor for exception org.anchoranalysis.feature.calculate.FeatureCalculationException
- FeatureCalculationException(Throwable) - Constructor for exception org.anchoranalysis.feature.calculate.FeatureCalculationException
- FeatureCalculationMap<S,T extends FeatureInput,U,E extends Exception> - Class in org.anchoranalysis.feature.calculate
-
Similar to a
FeatureCalculationbut stores several evaluations parameterised by a key. - FeatureCalculationMap(int) - Constructor for class org.anchoranalysis.feature.calculate.FeatureCalculationMap
-
Creates for a particular cache-size.
- FeatureCalculatorCachedMulti<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator.cached
-
A
FeatureCalculatorMultibut calculations are cached to avoid repetition if equalFeatureInputare passed. - FeatureCalculatorCachedMulti(FeatureCalculatorMulti<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
-
Creates a feature-calculator with a new cache
- FeatureCalculatorCachedMulti(FeatureCalculatorMulti<T>, int) - Constructor for class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
-
Creates a feature-calculator with a new cache
- FeatureCalculatorCachedSingle<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator.cached
-
A
FeatureCalculatorSinglebut calculations are cached to avoid repetition if equalFeatureInputare passed. - FeatureCalculatorCachedSingle(FeatureCalculatorSingle<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedSingle
-
Creates a feature-calculator with a new cache
- FeatureCalculatorCachedSingle(FeatureCalculatorSingle<T>, int) - Constructor for class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedSingle
-
Creates a feature-calculator with a new cache
- FeatureCalculatorFromProvider<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.task.feature.calculator
-
Calculates feature or feature values.
- FeatureCalculatorFromProvider(ProvidesStackInput, Optional<StackProvider>, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider
- FeatureCalculatorMulti<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session.calculator
-
Calculates one or more features for given params
- FeatureCalculatorMultiChangeInput<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator
-
Likes a SequentialSession but automatically changes parameters before calculation
- FeatureCalculatorMultiChangeInput(FeatureCalculatorMulti<T>, Consumer<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
-
Constructor
- FeatureCalculatorMultiFromSingle<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator
- FeatureCalculatorMultiFromSingle(FeatureCalculatorSingle<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
- FeatureCalculatorMultiReuse<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator
-
Remembers the first-calculation and always returns this value for all subsequent calculations
- FeatureCalculatorMultiReuse(FeatureCalculatorMulti<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
- FeatureCalculatorRepeated - Class in org.anchoranalysis.plugin.image.task.feature.calculator
- FeatureCalculatorSingle<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session.calculator
-
Calculates the result of a feature for particular params
- FeatureCalculatorSingleChangeInput<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator
-
Likes a SequentialSession but automatically changes parameters before calculation
- FeatureCalculatorSingleChangeInput(FeatureCalculatorSingle<T>, Consumer<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleChangeInput
- FeatureCalculatorSingleFromMulti<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.calculator
-
Exposes a
FeatureCalculatorMultias aFeatureCalculatorSingle - FeatureCalculatorSingleFromMulti(FeatureCalculatorMulti<T>) - Constructor for class org.anchoranalysis.feature.session.calculator.FeatureCalculatorSingleFromMulti
- FeatureConvertUnits<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical.convert
- FeatureConvertUnits() - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
- FeatureConvertUnits(Feature<T>, SpatialUnits.UnitSuffix) - Constructor for class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
- FeatureCostAssigner - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
- FeatureCostAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
- FeatureCSVMetadata - Class in org.anchoranalysis.feature.io.csv
-
What's needed to output a CSV other than the actual data items.
- FeatureCSVMetadata(String, List<String>) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
- FeatureCSVWriter - Class in org.anchoranalysis.feature.io.csv
-
Writes the results of feature-calculations as a CSV file.
- FeatureCSVWriter(CSVWriter) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureCSVWriter
- FeatureDeriveFromPair - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Base class for evaluating
FeaturePairObjectsin terms of another feature that operations on elements (first, second, merged etc.) - FeatureDeriveFromPair() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
- FeatureDeriveFromPair(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
- featureDescription(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
- featureDescription(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
- featureDescription(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
- featureDescription(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
- featureDescription(DeserializedManifest, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.NumberMarksFromManifest
- featureDescription(DeserializedManifest, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
- featureDescription(DeserializedManifest, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.TextFileAsIntegerFromManifest
- featureDescription(DeserializedManifest, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.TextFileAsIntegerFromPath
- featureDescription(T, Logger) - Method in class org.anchoranalysis.io.output.bean.ReportFeature
- FeatureDoubleElem<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
- FeatureDoubleElem() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
- FeatureEnergy<T extends FeatureInputEnergy> - Class in org.anchoranalysis.image.feature.bean
-
A base class for features that only require an input that extends from
FeatureInputEnergy - FeatureEnergy() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureEnergy
- FeatureEnergyChannel - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
A feature that uses a channel from the energy-stack as identified by an index
- FeatureEnergyChannel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
- FeatureEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.image.feature.bean.evaluator
-
Defines a feature and provides a means to calculate inputs for it, a session.
- FeatureEvaluator() - Constructor for class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
- FeatureHistogram - Class in org.anchoranalysis.image.feature.bean
- FeatureHistogram() - Constructor for class org.anchoranalysis.image.feature.bean.FeatureHistogram
- FeatureHistogramStatistic - Class in org.anchoranalysis.image.feature.histogram
- FeatureHistogramStatistic() - Constructor for class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
- FeatureInitParams - Class in org.anchoranalysis.feature.calculate
-
Parameters used to initialize a feature before any calculations
- FeatureInitParams() - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
- FeatureInitParams(Optional<KeyValueParams>, Optional<EnergyStackWithoutParams>, Optional<SharedObjects>) - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
- FeatureInitParams(SharedObjects) - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
- FeatureInitParams(KeyValueParams) - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
- FeatureInitParams(EnergyStack) - Constructor for class org.anchoranalysis.feature.calculate.FeatureInitParams
- FeatureInput - Interface in org.anchoranalysis.feature.input
-
A single input used for feature-calculation to produce a result.
- FeatureInputAllMemo - Class in org.anchoranalysis.mpp.feature.input.memo
- FeatureInputAllMemo(MemoCollection, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
- FeatureInputEnergy - Class in org.anchoranalysis.feature.input
- FeatureInputEnergy() - Constructor for class org.anchoranalysis.feature.input.FeatureInputEnergy
- FeatureInputEnergy(Optional<EnergyStack>) - Constructor for class org.anchoranalysis.feature.input.FeatureInputEnergy
- FeatureInputHistogram - Class in org.anchoranalysis.image.feature.histogram
- FeatureInputHistogram(Histogram, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.feature.histogram.FeatureInputHistogram
- FeatureInputMark - Class in org.anchoranalysis.mpp.feature.bean.mark
- FeatureInputMark(Mark, Optional<Dimensions>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
- FeatureInputMark(Mark, Optional<Dimensions>, Optional<KeyValueParams>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
- FeatureInputMark(Mark, Dimensions, KeyValueParams) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
- FeatureInputMarkCollection - Class in org.anchoranalysis.mpp.feature.bean.mark.collection
- FeatureInputMarkCollection(MarkCollection, Optional<Dimensions>) - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
- FeatureInputNull - Class in org.anchoranalysis.feature.input
- FeatureInputObjectCollection - Class in org.anchoranalysis.image.feature.object.input
- FeatureInputObjectCollection(ObjectCollection) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
- FeatureInputObjectCollection(ObjectCollection, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
- FeatureInputOverlappingCircleFixture - Class in org.anchoranalysis.test.feature.plugins.objects
- FeatureInputPairMemo - Class in org.anchoranalysis.mpp.feature.input.memo
- FeatureInputPairMemo(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
- FeatureInputPairObjects - Class in org.anchoranalysis.image.feature.object.input
-
A pair of objects (first and second) and maybe a merged version of both
- FeatureInputPairObjects(FeatureInputPairObjects) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
- FeatureInputPairObjects(ObjectMask, ObjectMask) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
- FeatureInputPairObjects(ObjectMask, ObjectMask, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
- FeatureInputPairObjects(ObjectMask, ObjectMask, Optional<EnergyStack>, Optional<ObjectMask>) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
- FeatureInputPairObjects(ObjectMask, ObjectMask, EnergyStack) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
- FeatureInputParams - Interface in org.anchoranalysis.feature.input
-
A feature-input that is associated with particular key-value parameters
- FeatureInputResults - Class in org.anchoranalysis.feature.input
- FeatureInputResults(ResultsVectorList, FeatureNameMapToIndex) - Constructor for class org.anchoranalysis.feature.input.FeatureInputResults
- FeatureInputSingleMemo - Class in org.anchoranalysis.mpp.feature.input.memo
- FeatureInputSingleMemo(VoxelizedMarkMemo, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
- FeatureInputSingleMemo(VoxelizedMarkMemo, EnergyStack) - Constructor for class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
- FeatureInputSingleObject - Class in org.anchoranalysis.image.feature.object.input
-
An input representing a single object-mask (with maybe an energy-stack associated)
- FeatureInputSingleObject(ObjectMask) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
- FeatureInputSingleObject(ObjectMask, Optional<EnergyStack>) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
- FeatureInputSingleObject(ObjectMask, EnergyStack) - Constructor for class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
- FeatureInputStack - Class in org.anchoranalysis.image.feature.stack
- FeatureInputStack() - Constructor for class org.anchoranalysis.image.feature.stack.FeatureInputStack
-
Should only be used if it's guaranteed the energy stack will be added later, as this this required.
- FeatureInputStack(Optional<EnergyStackWithoutParams>) - Constructor for class org.anchoranalysis.image.feature.stack.FeatureInputStack
-
Params without any ImageInitParams
- FeatureInputStack(EnergyStackWithoutParams) - Constructor for class org.anchoranalysis.image.feature.stack.FeatureInputStack
-
Params without any ImageInitParams
- FeatureInputType - Class in org.anchoranalysis.feature.input
-
Performs checks and aggregations on feature-input types are compatible with others
- FeatureInputWithResolution - Interface in org.anchoranalysis.feature.input
- FeatureIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
- FeatureIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
- FeatureIntersectingObjectsSingleElement - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
- FeatureIntersectingObjectsSingleElement() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
- FeatureIntersectingObjectsThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
- FeatureIntersectingObjectsThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold
- FeatureList<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
-
A list of features with the same input-type.
- FeatureList() - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList
-
Standard Bean Constructor.
- FeatureList(List<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList
-
Wraps an existing list
- FeatureList(Stream<Feature<T>>) - Constructor for class org.anchoranalysis.feature.bean.list.FeatureList
-
Creates a list from a stream
- FeatureListCSVGeneratorHorizontal - Class in org.anchoranalysis.feature.io.csv
-
CSV file where each feature is a column (spanning horizontally).
- FeatureListCSVGeneratorHorizontal(String, FeatureNameList) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureListCSVGeneratorHorizontal
-
Creates without setting any results (i.e.
- FeatureListCSVGeneratorVertical - Class in org.anchoranalysis.feature.io.csv
-
CSV file where each feature is a row (spanning vertically).
- FeatureListCSVGeneratorVertical(String, FeatureNameList) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureListCSVGeneratorVertical
-
Creates without setting any results (i.e.
- FeatureListElem<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
- FeatureListElem() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureListElem
- FeatureListElem(FeatureList<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureListElem
-
Constructor
- FeatureListEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.image.feature.bean.evaluator
-
Defines a list of features and provides a means to calculate inputs for it, a session.
- FeatureListEvaluator() - Constructor for class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator
- FeatureListFactory - Class in org.anchoranalysis.feature.bean.list
-
Factory for creating
FeatureListin different ways - FeatureListProvider<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
- FeatureListProvider() - Constructor for class org.anchoranalysis.feature.bean.list.FeatureListProvider
- FeatureListProviderAggregatePair - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
Calculates features on each part of a pair (first, second, merged etc.) and then reduces the calculation to a single number.
- FeatureListProviderAggregatePair() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
- FeatureListProviderLDAClassifier<T extends FeatureInput> - Class in org.anchoranalysis.plugin.ml.bean.classifier
- FeatureListProviderLDAClassifier() - Constructor for class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderLDAClassifier
- FeatureListProviderSVMClassifier - Class in org.anchoranalysis.plugin.ml.bean.classifier
- FeatureListProviderSVMClassifier() - Constructor for class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
- FeatureListStoreUtilities - Class in org.anchoranalysis.feature.list
- FeatureMark - Class in org.anchoranalysis.mpp.feature.bean.mark
- FeatureMark() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.FeatureMark
- FeatureMarkCollection - Class in org.anchoranalysis.mpp.feature.bean.mark.collection
- FeatureMarkCollection() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureMarkCollection
- FeatureMarkDirection - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
- FeatureMarkDirection() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
- FeatureMarkEccentricity - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
- FeatureMarkEccentricity() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.FeatureMarkEccentricity
- FeatureMarkRegion - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
- FeatureMarkRegion() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.FeatureMarkRegion
- FeatureNameList - Class in org.anchoranalysis.feature.name
-
A list of Strings representing feature names
- FeatureNameList() - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
- FeatureNameList(String) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
- FeatureNameList(Set<String>) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
- FeatureNameList(Stream<String>) - Constructor for class org.anchoranalysis.feature.name.FeatureNameList
- FeatureNameMapToIndex - Class in org.anchoranalysis.feature.name
-
A map of Feature-Names (Strings) to indexes (Int)
- FeatureNameMapToIndex() - Constructor for class org.anchoranalysis.feature.name.FeatureNameMapToIndex
- featureNamesNonAggregate() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterMetadata
-
Names of each feature in the feature columns.
- FeatureObjectCollection - Class in org.anchoranalysis.image.feature.bean.object.collection
- FeatureObjectCollection() - Constructor for class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
- FeatureOperator<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
-
Base class for features that broadly accept any type of feature-input.
- FeatureOperator() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureOperator
- FeaturePairMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element
- FeaturePairMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeaturePairMemo
- FeaturePairMemoOne - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
- FeaturePairMemoOne() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoOne
- FeaturePairMemoSingleRegion - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
- FeaturePairMemoSingleRegion() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
- FeaturePairObjects - Class in org.anchoranalysis.image.feature.bean.object.pair
- FeaturePairObjects() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.FeaturePairObjects
- FeatureProvider<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.provider
- FeatureProvider() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProvider
- FeatureProviderBean<B,P> - Class in org.anchoranalysis.feature.bean.provider
- FeatureProviderBean() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderBean
- FeatureProviderDefine<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.provider
- FeatureProviderDefine() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
- FeatureProviderDefine(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
- FeatureProviderReference - Class in org.anchoranalysis.feature.bean.provider
- FeatureProviderReference() - Constructor for class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
- FeatureRelatedBean<T> - Class in org.anchoranalysis.feature.bean
-
Beans-related to features that require initialization with
SharedFeaturesInitParams - FeatureRelatedBean() - Constructor for class org.anchoranalysis.feature.bean.FeatureRelatedBean
- FeatureResults - Class in org.anchoranalysis.feature.bean.results
-
Features that process
ResultsVectorList. - FeatureResults() - Constructor for class org.anchoranalysis.feature.bean.results.FeatureResults
- FeatureResultSupplier - Interface in org.anchoranalysis.plugin.operator.feature.score
-
Supplies the result of a feature-calculation
- features() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- FeatureSession - Class in org.anchoranalysis.feature.session
-
A single-point in the code for creating feature-sessions (a factory).
- FeatureSessionCache<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
-
A context in which to calculate features while caching certain duplicated internal calculations among the features.
- FeatureSessionCacheFactory - Interface in org.anchoranalysis.feature.session.cache
- FeatureSessionCalculator<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
-
Calculates features in the context of a particular feature-session.
- FeaturesFromXmlFixture - Class in org.anchoranalysis.test.feature.plugins
- FeatureSingleMemo - Class in org.anchoranalysis.mpp.feature.bean.energy.element
- FeatureSingleMemo() - Constructor for class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
- FeatureSingleMemoRegion - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
- FeatureSingleMemoRegion() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
- FeatureSingleObject - Class in org.anchoranalysis.image.feature.bean.object.single
- FeatureSingleObject() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject
- FeatureSingleObjectFromShared<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
-
Calculates as object-masks from entities in shared, using the feature-input only for a energy-stack.
- FeatureSingleObjectFromShared() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
- FeatureSource<T extends InputFromManager,S,U extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source
-
Extracts features from some kind of inputs to produce one or more rows in a feature-table.
- FeatureSource() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
- FeatureStack - Class in org.anchoranalysis.image.feature.bean.stack
- FeatureStack() - Constructor for class org.anchoranalysis.image.feature.bean.stack.FeatureStack
- FeatureSymbolCalculator<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
-
Resolves and calculates a feature by a symbol (an ID/variable-name referring to another feature)
- FeatureTableCalculator<T extends FeatureInput> - Interface in org.anchoranalysis.image.feature.session
-
A feature-calculator with additional functions for encoding the output in in a tabular-format with column-names
- FeatureTableCSVGenerator<T> - Class in org.anchoranalysis.feature.io.csv
-
Base class for a
Generatorthat outputs a feature-table in CSV format. - FeatureTableCSVGenerator(String, List<String>) - Constructor for class org.anchoranalysis.feature.io.csv.FeatureTableCSVGenerator
-
Creates for a particular manifest-function and headers.
- FeatureTestCalculator - Class in org.anchoranalysis.test.feature.plugins
- FeatureTestCalculatorDuo - Class in org.anchoranalysis.test.feature.plugins
-
Tests that consider two possibilities: positive and negative
- featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
- featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
- featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
- featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfOutsideRange
- featureToCalcInputVal() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
-
Which feature to calculate the input-value? The result is then passed to
RangeCompareBase.calculateForValue(double, org.anchoranalysis.feature.calculate.cache.SessionInput<T>) - FeatureUnary<T extends FeatureInput,S extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
-
A feature that contains another feature as a bean-parameter.
- FeatureUnary() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnary
- FeatureUnary(Feature<S>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnary
- FeatureUnaryGeneric<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
-
A
FeatureUnarythat accepts any {#linkFeatureInput} irrespective of type. - FeatureUnaryGeneric() - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnaryGeneric
- FeatureUnaryGeneric(Feature<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.FeatureUnaryGeneric
- FeatureValueCheckMark<T extends FeatureInput> - Class in org.anchoranalysis.plugin.mpp.bean.check
- FeatureValueCheckMark() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- FeatureValueIndividualEnergyGreaterThan - Class in org.anchoranalysis.plugin.mpp.bean.check
- FeatureValueIndividualEnergyGreaterThan() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueIndividualEnergyGreaterThan
- FeatureValueMarkGreaterEqualThan - Class in org.anchoranalysis.plugin.mpp.bean.check
- FeatureValueMarkGreaterEqualThan() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueMarkGreaterEqualThan
- FeedbackBeginParameters<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback
- FeedbackBeginParameters() - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- FeedbackEndParameters<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback
- FeedbackEndParameters(T, MessageLogger) - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
- FeedbackReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback
- FeedbackReceiverBean<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
- FeedbackReceiverBean() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverBean
- FeedbackReceiverList<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
- FeedbackReceiverList() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
- FeedbackReceiverRequireArguments<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
- FeedbackReceiverRequireArguments() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
- fetchUnmatchedWorker() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
- fields() - Method in class org.anchoranalysis.bean.AnchorBean
-
A list of all bean-fields that are associated with this bean directly (fields of children are not checked).
- FileDetails - Class in org.anchoranalysis.plugin.io.multifile
- FileDetails(Path, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Constructor for class org.anchoranalysis.plugin.io.multifile.FileDetails
- fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.PNG
- fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.Tiff
- fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMETiff
- fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMEXML
- fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.Tiff
- fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
- fileExtension(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
- fileInputManager() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
- FileLabelMap<T> - Class in org.anchoranalysis.image.experiment.label
- FileLabelMap() - Constructor for class org.anchoranalysis.image.experiment.label.FileLabelMap
- FileMatch - Class in org.anchoranalysis.io.manifest.finder.match
- filePath() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- FilePath - Class in org.anchoranalysis.plugin.io.bean.filepath
- FilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.FilePath
- FilePathAppendBase - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
- FilePathAppendBase() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
- FilePathBaseAppendToManager - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
- FilePathBaseAppendToManager() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManager
- FilePathBaseAppendToManagerWithFileID - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
- FilePathBaseAppendToManagerWithFileID() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManagerWithFileID
- FilePathCounter - Class in org.anchoranalysis.io.output.bean.path.prefixer
- FilePathCounter() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
- FilePathCounter(String) - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
- FilePathParser - Class in org.anchoranalysis.plugin.io.bean.groupfiles.parser
- FilePathParser() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
- FilePathPattern - Class in org.anchoranalysis.plugin.io.bean.summarizer.path
-
Converts a list of file-paths into a form that tries to find a pattern in the naming style using the path-pattern-finder library
- FilePathPattern() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
- FilePathPrefixerContext - Class in org.anchoranalysis.io.output.path.prefixer
- FilePathPrefixerContext(boolean, Optional<Path>) - Constructor for class org.anchoranalysis.io.output.path.prefixer.FilePathPrefixerContext
- FilePathResolver - Class in org.anchoranalysis.launcher
- FilePathResolver(Class<?>) - Constructor for class org.anchoranalysis.launcher.FilePathResolver
- FilePathToUnixStyleConverter - Class in org.anchoranalysis.core.system.path
-
Conversion to Unix-style separators
- FileSetFromStringSet - Class in org.anchoranalysis.plugin.io.bean.provider.file
- FileSetFromStringSet() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.FileSetFromStringSet
- FileSizeStatistics - Class in org.anchoranalysis.plugin.io.bean.summarizer.path
-
Tracks the range of file-size.
- FileSizeStatistics() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.path.FileSizeStatistics
- FileType - Class in org.anchoranalysis.io.manifest.file
- FileType(ManifestDescription, String) - Constructor for class org.anchoranalysis.io.manifest.file.FileType
- fill(BinaryVoxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.plugin.imagej.mask.ApplyImageJMorphologicalOperation
- FillHoles - Class in org.anchoranalysis.plugin.imagej.bean.mask.provider
- FillHoles - Class in org.anchoranalysis.plugin.imagej.bean.object.provider
-
Fills holes in an object.
- FillHoles() - Constructor for class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
- FillHoles() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
- filter(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Filters a
ObjectCollectionto include certain items based on a predicate - filter(Stream<T>, Class<? extends Exception>, CheckedPredicate<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
-
Performs a
Stream.filter(java.util.function.Predicate<? super T>)but accepts a predicate that can throw a checked-exception - filter(CheckedPredicate<ObjectMask, E>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Filters a
ObjectCollectionto include certain items based on a predicate - and optionally store rejected objects. - filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.object.ObjectFilter
-
Filters an object-collection to remove objects according to a criteria
- filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.And
- filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.Or
- filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
- filter(ObjectCollection, Optional<Dimensions>, Optional<ObjectCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
- Filter - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
- Filter - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Applies an object-filter to the results of an upstream segmentation.
- Filter() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.Filter
- Filter() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
- filterAndMap(Predicate<Feature<T>>, CheckedFunction<Feature<T>, Feature<S>, E>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- filterAndMap(Predicate<ObjectMask>, UnaryOperator<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Performs a
ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>)and then aObjectMaskStream.map(org.anchoranalysis.core.functional.checked.CheckedFunction<org.anchoranalysis.image.voxel.object.ObjectMask, org.anchoranalysis.image.voxel.object.ObjectMask, E>). - filterAndMapFrom(Iterable<T>, Predicate<T>, CheckedFunction<T, ObjectWithProperties, E>) - Static method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithPropertiesFactory
-
Creates a new collection by filtering an iterable and then mapping it to
ObjectWithProperties - filterAndMapFrom(Iterable<T>, Predicate<T>, CheckedFunction<T, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection by filtering an iterable and then mapping it to
ObjectMask - filterAndMapToList(List<S>, Predicate<S>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Creates a new collection by filtering a list and then mapping to a list of another type.
- filterAndMapWithIndexFrom(List<T>, Predicate<T>, CheckedBiFunction<T, Integer, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection by filtering a list and then mapping from it to
ObjectMask. - filterAndMapWithIndexToList(List<S>, Predicate<S>, CheckedBiFunction<S, Integer, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Creates a new collection by filtering a list and then mapping (with an index) to a list of another type.
- FilterByGroup - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
- FilterByGroup() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
- FilterCsvColumn<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter
-
Finds a CSV file with the names of an input as the first-column.
- FilterCsvColumn() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
- FilterDescriptiveName<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter
-
Filters all the input objects for only those with certain types of descriptive-names.
- FilterDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
- FilterDescriptiveNameEqualsContains - Class in org.anchoranalysis.plugin.io.input.filter
-
Filters a list of input-objects by the descriptive name
- FilterDescriptiveNameEqualsContains(String, String) - Constructor for class org.anchoranalysis.plugin.io.input.filter.FilterDescriptiveNameEqualsContains
-
Constructor
- filterExclude(Predicate<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Filters a
ObjectCollectionto exclude certain items based on a predicate - FilterForExistingFiles - Class in org.anchoranalysis.plugin.io.bean.input.files.provider
- FilterForExistingFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
- FilterHelper - Class in org.anchoranalysis.plugin.imagej.channel.provider
- FilterIfDebug<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input.filter
-
Filters a list of inputs when in debug-mode
- FilterIfDebug() - Constructor for class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
- filterSubset(Predicate<ObjectMask>, List<Integer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Like
ObjectMaskStream.filter(java.util.function.Predicate<org.anchoranalysis.image.voxel.object.ObjectMask>)but only operates on certain indices of the collection. - filterToList(Collection<T>, Class<? extends Exception>, CheckedPredicate<T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Filters a collection and maps the result to a list
- filterToList(Collection<T>, Predicate<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Filters a collection and maps the result to a list
- finalizeBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
- finalizeBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityByteBuffer
- finalizeBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityShortBuffer
- Findable<T> - Interface in org.anchoranalysis.annotation.io.image.findable
- findArbitraryOnVoxel() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Finds any arbitrary "ON" voxel on the object.
- FindChildStrategy - Interface in org.anchoranalysis.feature.session.strategy.child
- findClosestResult(Point3i) - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
- FindCommonVoxelType - Class in org.anchoranalysis.image.voxel.datatype
-
Finds a common voxel-data type to represent two types.
- findDirectory(List<MutableDirectory>, Predicate<MutableDirectory>) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
- Finder - Interface in org.anchoranalysis.io.manifest.finder
- FinderExperimentFileDirectories - Class in org.anchoranalysis.io.manifest.finder
- FinderExperimentFileDirectories() - Constructor for class org.anchoranalysis.io.manifest.finder.FinderExperimentFileDirectories
- FinderFileAsText - Class in org.anchoranalysis.io.manifest.finder
- FinderFileAsText(String, ErrorReporter) - Constructor for class org.anchoranalysis.io.manifest.finder.FinderFileAsText
- FinderKeyValueParams - Class in org.anchoranalysis.io.manifest.finder
- FinderKeyValueParams(String, ErrorReporter) - Constructor for class org.anchoranalysis.io.manifest.finder.FinderKeyValueParams
- FinderSerializedObject<T> - Class in org.anchoranalysis.io.manifest.finder
- FinderSerializedObject(String, ErrorReporter) - Constructor for class org.anchoranalysis.io.manifest.finder.FinderSerializedObject
- FinderSingleDirectory - Class in org.anchoranalysis.io.manifest.finder
- FinderSingleDirectory() - Constructor for class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
- FinderSingleFile - Class in org.anchoranalysis.io.manifest.finder
- FinderSingleFile(ErrorReporter) - Constructor for class org.anchoranalysis.io.manifest.finder.FinderSingleFile
- FinderUtilities - Class in org.anchoranalysis.io.manifest.finder
- FindFailedException - Exception in org.anchoranalysis.io.manifest.finder
- FindFailedException(String) - Constructor for exception org.anchoranalysis.io.manifest.finder.FindFailedException
- FindFailedException(Throwable) - Constructor for exception org.anchoranalysis.io.manifest.finder.FindFailedException
- findFieldsOfClass(Class<?>) - Method in class org.anchoranalysis.bean.AnchorBean
-
Finds all bean-fields that are instances of a certain class.
- findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class org.anchoranalysis.io.manifest.directory.JobRootDirectory
- findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
- findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
- findFile(List<OutputtedFile>, Predicate<OutputtedFile>, boolean) - Method in class org.anchoranalysis.io.manifest.directory.Subdirectory
- findFile(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderFileAsText
- findFile(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderKeyValueParams
- findFile(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderSerializedObject
- findFile(Manifest) - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleFile
- findFileFromIndex(List<OutputtedFile>, String, boolean) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
- findFileFromIndex(List<OutputtedFile>, String, boolean) - Method in interface org.anchoranalysis.io.manifest.directory.sequenced.SequencedDirectory
- findIndex(String) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- findListFile(Manifest, Predicate<OutputtedFile>) - Static method in class org.anchoranalysis.io.manifest.finder.FinderUtilities
- findListFolder(Manifest, Predicate<MutableDirectory>) - Static method in class org.anchoranalysis.io.manifest.finder.FinderUtilities
- findMatch(ObjectCollection) - Method in class org.anchoranalysis.image.bean.object.ObjectMatcher
-
Finds matches for objects
- findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
- findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
- findMatch(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection
- findMaxPriority() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
- FindMinimumDistance - Class in org.anchoranalysis.image.core.outline.traverser.visited.combine
-
TODO naming is too complicated in functions with lots of min/max
- findMostDeepCombinableException() - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
-
Traverses through the nested-exceptions and finds the most deep exception that is combinable using the rules about combining and skipping outlined in the class description
- findObjectsMatchingRow(ObjectCollectionRTree) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
- findObjectsMatchingRow(CSVRow, ObjectCollectionRTree) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
- findObjectsMatchingRow(CSVRow, ObjectCollectionRTree) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
- findObjectsMatchingRow(CSVRow, ObjectCollectionRTree) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
- findObjectsWithIntersectingBBox(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- findOptimum(KernelProposer<S>, ListUpdatableMarkSetCollection, FeedbackReceiver<S>, OptimizationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
- findOptimum(KernelProposer<U>, ListUpdatableMarkSetCollection, FeedbackReceiver<S>, OptimizationContext) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.OptimizationScheme
-
Finds an optimal state
- findOptimum(KernelProposer<U>, ListUpdatableMarkSetCollection, FeedbackReceiver<S>, OptimizationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
- FindOutline - Class in org.anchoranalysis.image.core.outline
-
Finds outline voxels i.e.
- FindPointOnOutline - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline
-
Finds a pixel on the outline of an object in a particular direction
- FindPointOnOutline() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutline
- FindPointOnOutlineWalk - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline
-
Walks in a particular direction until the outline is found.
- FindPointOnOutlineWalk() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
- findRoot(String, boolean) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap
-
Finds a root to match a name and debug/status
- findSingleItem(Manifest, Predicate<OutputtedFile>) - Static method in class org.anchoranalysis.io.manifest.finder.FinderUtilities
- first() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
-
For recording first-level outputs.
- first() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
- First - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Evaluates the first-object in a pair only
- First() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.First
- First(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.First
- FIRST - org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
- firstConnectedTo(ContourList) - Method in class org.anchoranalysis.plugin.points.contour.ContourList
- firstLevelContains(String) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
- firstPart() - Method in class org.anchoranalysis.feature.io.name.CombinedName
- firstPart() - Method in interface org.anchoranalysis.feature.io.name.MultiName
-
The first part, and grouping key.
- firstPart() - Method in class org.anchoranalysis.feature.io.name.SimpleName
- firstPart() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
- firstPartWithCustomMiddle(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
- firstPartWithDataset() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
-
The first-part of the out-path string including the dataset of the current experiment as a folder
- firstPartWithFilename() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
-
The first-part of the out-path string including the file-name of the previous experiment as a folder
- FirstSecondOrderStatistic - Class in org.anchoranalysis.math.statistics
- FirstSecondOrderStatistic() - Constructor for class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
- fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.mpp.bean.points.fitter.PointsFitter
- fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
- fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
- fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
- fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
- fit(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
- FitBoxToOnVoxels - Class in org.anchoranalysis.plugin.image.bean.mask.provider.resize
-
Fits a box around the ON pixels.
- FitBoxToOnVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.resize.FitBoxToOnVoxels
- fitMarkToPointsFromMarks(MarkCollection, Dimensions) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
-
Extract points from a marks, creates a new mark from markProvider and then fits this mark the extracted points
- FitPoints - Class in org.anchoranalysis.plugin.points.bean.mark.proposer.single
- FitPoints() - Constructor for class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
- fitPointsToMark(List<Point3f>, Mark, Dimensions) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
- FitResult - Class in org.anchoranalysis.plugin.points.bean.fitter
- FitResult() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- flagForNoRegion() - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
- flagForRegion(int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
- flagForRegion(int, int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
-
Combines two regions
- flagForRegion(int, int, int) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
-
Combines three regions
- flags() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- flatBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
- flatMap(Class<? extends Exception>, CheckedFunction<ObjectMask, ObjectCollection, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Like a typical
flatMap()operation but accepts a mapping function that throws a checked exception. - flatMap(Function<ObjectMask, ObjectCollection>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Creates a new
ObjectCollectionafter mapping each item to several others. - flatMap(Optional<S>, CheckedFunction<S, Optional<T>, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
-
Like
Optional.flatMap(java.util.function.Function<? super T, ? extends java.util.Optional<? extends U>>)but tolerates an exception in the mapping function, which is immediately thrown. - flatMap(Stream<S>, Class<? extends Exception>, CheckedFunction<S, Collection<? extends T>, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
-
Performs a
Stream.flatMap(java.util.function.Function<? super T, ? extends java.util.stream.Stream<? extends R>>)but accepts a function that can throw a checked-exception - flatMapFrom(Collection<T>, Function<T, ObjectCollection>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection by flatMapping an incoming stream to
ObjectCollection - flatMapFrom(Stream<T>, Class<? extends Exception>, CheckedFunction<T, ObjectCollection, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection by flatMapping an incoming stream to
ObjectCollectionAND rethrowing any exception during mapping - flatMapFromCollection(Stream<T>, Class<? extends Exception>, CheckedFunction<T, Collection<? extends ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new
ObjectCollectionby flatMapping an incoming stream toCollection<ObjectMask>AND rethrowing any exception during mapping - flatMapFromOptional(Iterable<S>, CheckedFunction<S, Optional<FeatureList<T>>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
-
Creates a new feature-list by flat-mapping an iterable to an optional feature
- flatMapFromRange(int, int, Class<? extends Exception>, CheckedIntFunction<ObjectCollection, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection by flat-mapping integers (from a range) each to a
ObjectCollection - flatMapFromRange(int, int, IntFunction<ObjectCollection>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection by flat-mapping integers (from a range) each to a
ObjectCollection - flatMapToList(Collection<S>, Function<S, Stream<T>>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Flat-maps a collection to a list where in the original collection can produce many elements in the outging list.
- FlattenAsChannel - Class in org.anchoranalysis.plugin.io.bean.stack.reader
-
Combines all series and frames returned by a reader by converting them into multiple channels in the same image
- FlattenAsChannel() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
- flattenZ() - Method in class org.anchoranalysis.image.core.mask.Mask
- flattenZ() - Method in interface org.anchoranalysis.image.core.object.seed.Seed
- flattenZ() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- flattenZ() - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
- flattenZ() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
A maximum-intensity projection (flattens in z dimension)
- flattenZ() - Method in class org.anchoranalysis.spatial.box.BoundingBox
- flattenZ() - Method in class org.anchoranalysis.spatial.Extent
-
Collapses the Z dimension i.e.
- FlattenZ - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice
-
Flattens a mask in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
- FlattenZ - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice
-
Flattens all object-masks in the z-dimension, so it is 2D instead of 3D (like a maximum intensity projection).
- FlattenZ() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.slice.FlattenZ
- FlattenZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.FlattenZ
- floatArray(float[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
-
Wraps an float-array into a voxel-buffer.
- floatBuffer(FloatBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
-
Wraps a float buffer into a voxel-buffer.
- floatFromDouble(Point3d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- floatFromInt(Point2i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- floatFromInt(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- floatFromIntDropZ(ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.PointConverter
-
Creates a new
Point3fwith X, Y values from thePoint3ibut setting Z to be 0 - FloatFromUnsignedByte - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat
- FloatFromUnsignedByte() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedByte
- FloatFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat
- FloatFromUnsignedInt(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tofloat.FloatFromUnsignedInt
- FloatUtilities - Class in org.anchoranalysis.math.arithmetic
-
Utilities for arithmetic operations involving type
float - FloatVoxelType - Class in org.anchoranalysis.image.voxel.datatype
- FloodFillEachIntensityLevel - Class in org.anchoranalysis.plugin.imagej.bean.object.segment
-
Creates an object for each separate intensity-value (beginning at
startingColor) by flood-filling. - FloodFillEachIntensityLevel() - Constructor for class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
- forBoxes(BoundingBox, BoundingBox) - Static method in class org.anchoranalysis.plugin.image.box.IntersectionOverUnion
-
Calculates the intersection-over-union score a pair of bounding-boxes.
- ForceBitsPerPixel - Class in org.anchoranalysis.io.bioformats.bean.options
- ForceBitsPerPixel() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
- ForceChannelsPerByteArray - Class in org.anchoranalysis.io.bioformats.bean.options
- ForceChannelsPerByteArray() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceChannelsPerByteArray
- ForceNumberChannels - Class in org.anchoranalysis.io.bioformats.bean.options
- ForceNumberChannels() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
- ForceNumberFrames - Class in org.anchoranalysis.io.bioformats.bean.options
- ForceNumberFrames() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
- ForceTimeSeriesToStack - Class in org.anchoranalysis.io.bioformats.bean.options
-
Treats a time-series as if it was a z-stack
- ForceTimeSeriesToStack() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
- forChild() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
-
Performs calculations not on the main cache, but on a child cache
- forChild() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
- forEach(Stream<T>, Class<? extends Exception>, CheckedConsumer<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
-
Performs a
Stream.forEach(java.util.function.Consumer<? super T>)but accepts a consumer that can throw a checked-exception - forEach(CheckedBiConsumer<String, StoreSupplier<Stack>, E>) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
-
Iterates over each entry in the map.
- forList(List<Point3i>) - Static method in class org.anchoranalysis.image.core.points.BoundingBoxFromPoints
-
Create from a list of points
- ForSpecificAxis<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
-
Dimensions-calculation for one specific axis only.
- ForSpecificAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
- forTwoPoints(Point3d, Point3d) - Static method in class org.anchoranalysis.image.core.points.BoundingBoxFromPoints
-
Creates a bounding-box for two unordered points.
- Found<T> - Class in org.anchoranalysis.annotation.io.image.findable
-
A positive-result when an object is found.
- Found(T) - Constructor for class org.anchoranalysis.annotation.io.image.findable.Found
- FrequencyMap<T> - Class in org.anchoranalysis.plugin.io.summarizer
-
Counts the frequency of certain strings, and describes the contents in human language.
- FrequencyMap() - Constructor for class org.anchoranalysis.plugin.io.summarizer.FrequencyMap
- friendlyMessage() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
- friendlyMessage() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
- friendlyMessage() - Method in interface org.anchoranalysis.core.exception.friendly.HasFriendlyErrorMessage
-
A friendly message to describe to the user what went wrong.
- friendlyMessageHierarchy() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
- friendlyMessageHierarchy() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
- friendlyMessageHierarchy() - Method in interface org.anchoranalysis.core.exception.friendly.HasFriendlyErrorMessage
-
A friendly message to describe to the user what went wrong, which doesn't impose a fixed-size, or showExceptionNames
- friendlyMessageHierarchy(Writer, int, boolean) - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
- friendlyMessageHierarchy(Writer, int, boolean) - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyRuntimeException
- friendlyMessageHierarchy(Writer, int, boolean) - Method in interface org.anchoranalysis.core.exception.friendly.HasFriendlyErrorMessage
-
A friendly message to describe to the user what went wrong, including all nested exceptions that have a non-empty error message
- from(Feature<T>...) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
-
Creates a list for one or more features
- from(Channel) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus
-
Creates an
ImagePlusfrom aChannel. - from(Stack, boolean) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus
-
Creates an
ImagePlusfrom aStack. - from(VoxelsWrapper) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
-
Converts from a
VoxelsWrapper(Anchor structure) to aImg(ImgLib2 structure). - from(VoxelsWrapper) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus
-
Creates an
ImagePlusfrom aVoxelsWrapper. - from(VoxelsWrapper, int) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor
-
Creates a
ImageProcessorby extracting a slice from aVoxelsWrapper. - FromAnnotations<T extends AnnotatorStrategy> - Class in org.anchoranalysis.plugin.annotation.bean.file
- FromAnnotations() - Constructor for class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
- fromByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
- fromByte(VoxelBuffer<UnsignedByteBuffer>, Extent) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor
-
Creates a
ImageProcessorfrom voxel-buffer (of typeByteBuffer) that is already a slice. - fromByte(SliceBufferIndex<UnsignedByteBuffer>, int) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor
- fromByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
- fromByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg
- FromByte - Class in org.anchoranalysis.image.voxel.factory.sliceindex
- FromChannel - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider
-
Creates image-dimensions by referencing them from a ChannelProvider
- FromChannel - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
- FromChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert
-
Creates a mask from an existing channel, reusing the channel's buffer and considering all 0 values as OFF, and 255 values as ON
- FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
- FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
- FromChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromChannel
- FromChannelBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
Base-class for mask-providers that accept a channel as input
- FromChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
- FromChannelOrMask - Class in org.anchoranalysis.plugin.image.bean.stack.provider
-
Creates a stack from a channel or mask (reusing the voxel buffers)
- FromChannelOrMask() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
- FromChannelOrMask(ChannelProvider) - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
- FromCSVInput - Class in org.anchoranalysis.plugin.mpp.experiment.objects
- FromCSVInput(MultiInput, Path) - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
- FromCSVInputManager - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects
- FromCSVInputManager() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
- FromCSVSharedState - Class in org.anchoranalysis.plugin.mpp.experiment.objects
-
Shared-state for
ExportObjectsFromCSV - FromCSVSharedState() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVSharedState
- FromDescriptiveName - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
-
The prefixer uses a combination of a out-path-prefix and the descriptive-name of inputs to create an output prefix
- FromDescriptiveName() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.FromDescriptiveName
- FromDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider
- FromDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider
- FromDimensionsBase<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
- FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
- FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
- FromDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.FromDimensionsBase
- FromDualVoxelizedMarks - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
- FromDualVoxelizedMarks() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromDualVoxelizedMarks
- FromEntries - Class in org.anchoranalysis.plugin.io.bean.channel.map
- FromEntries() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
- fromFloat(VoxelBuffer<FloatBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
- fromFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
- fromFloat(Voxels<FloatBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg
- FromFloat - Class in org.anchoranalysis.image.voxel.factory.sliceindex
- FromHistogram - Class in org.anchoranalysis.plugin.image.task.bean.feature.source
-
Each input-file describes a histogram that produces one row of features.
- FromHistogram() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
- FromImage - Class in org.anchoranalysis.plugin.image.task.bean.feature.source
-
An image that produces one row of features.
- FromImage() - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
- FromInput - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
Finds the input-stack using a conventional name of
input_image- and extracts the first channel - FromInput - Class in org.anchoranalysis.plugin.image.bean.stack.provider
-
Finds the input-stack using a conventional name of
input_image - FromInput() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
- FromInput() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
- FromInt - Class in org.anchoranalysis.image.voxel.factory.sliceindex
- fromIterable(Iterable<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
-
Creates a list of features from an iterable
- FromList - Class in org.anchoranalysis.bean.shared.color.scheme
-
Specifies a list of colors by a list.
- FromList() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.FromList
- FromMarkProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
- FromMarkProposer() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
- FromMarks - Class in org.anchoranalysis.plugin.mpp.bean.object.provider
-
Creates object-masks from a
MarkCollectionwhere (a particular region of) each mark creates an object. - FromMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
- FromMask - Class in org.anchoranalysis.overlay.object.scaled
- FromMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask
- FromMask - Class in org.anchoranalysis.plugin.image.bean.object.provider.mask
-
Converts a binary-mask to an object-collection (containing a single object)
- FromMask() - Constructor for class org.anchoranalysis.overlay.object.scaled.FromMask
- FromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMask
- FromMask() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
- FromMaskBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask
-
A base class for a
ChannelProviderwhich also uses a binary-mask, but which doesn't use any otherChannelProvideras an input. - FromMaskBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
- FromMetadata - Class in org.anchoranalysis.plugin.io.bean.channel.map
- FromMetadata() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.FromMetadata
- fromObject(ObjectMask) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat
- FromObjects - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert
-
Creates a
Maskfrom a collection of object-masks - FromObjects - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
- FromObjects<T extends FeatureInput> - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.source
-
Extracts features for each object in a collection.
- FromObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
- FromObjects() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
- FromObjects() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- FromOutputName - Class in org.anchoranalysis.plugin.io.bean.descriptivename
- FromOutputName() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.FromOutputName
- FromParamsBase - Class in org.anchoranalysis.plugin.image.feature.bean.score
- FromParamsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.FromParamsBase
- fromPhysicalArea(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
-
Converts from physical-area to pixels.
- fromPhysicalArea(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
-
Converts from physical-area to pixels.
- fromPhysicalDistance(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
-
Converts from physical-distance to voxels.
- fromPhysicalDistance(double, DirectionVector) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
-
Converts from physical-distance to voxels.
- fromPhysicalVolume(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
-
Converts from physical-volume to voxels.
- fromPhysicalVolume(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
-
Converts from physical-volume to voxels.
- fromProvider(Provider<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
-
Creates a list for a single-feature created from a provider
- FromProvider - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
- FromProvider() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
- fromProviders(Collection<FeatureProvider<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
-
Creates a list of features from a collection of feature-providers
- fromRepeated(int, Supplier<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection by repeatedly calling a function to create a single
ObjectMask - FromSerializedMarks - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
- FromSerializedMarks() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
- FromSerializedObject - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
- FromSerializedObject() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
- fromSet(Set<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection from a set of
ObjectMask - fromShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
- fromShort(VoxelBuffer<UnsignedShortBuffer>, Extent) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor
-
Creates a
ImageProcessorfrom voxel-buffer (of typeShortBuffer) that is already a slice. - fromShort(SliceBufferIndex<UnsignedShortBuffer>, int) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImageProcessor
- fromShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
- fromShort(Voxels<UnsignedShortBuffer>) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToNativeImg
- FromShort - Class in org.anchoranalysis.image.voxel.factory.sliceindex
- FromSingle - Class in org.anchoranalysis.bean.shared.color.scheme
-
A single color repeated to meet the size.
- FromSingle() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.FromSingle
- FromSingleMark - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
- FromSingleMark() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
- fromSlice(Voxels<UnsignedByteBuffer>, int, String) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertToImagePlus
-
Creates an
ImagePlusfrom one slice of aVoxels<UnsignedByteBuffer> voxels. - fromSlice(VoxelsWrapper, int) - Static method in class org.anchoranalysis.image.voxel.convert.imglib2.ConvertToImg
- fromStack(Stack) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat
- FromStack - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
Extracts a channel from a provider of a stack
- FromStack() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
- FromStack(ProviderAsStack) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
- FromStackChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.convert
- FromStackChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
- FromStacks - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects a a subset of channels from a set of stacks
- FromStacks() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.FromStacks
- fromStream(Stream<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
-
Creates a list of features from a stream
- FromUnitValueDistance - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
- FromUnitValueDistance() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
- FromVoxelizedMarksWithEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
- FromVoxelizedMarksWithEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.FromVoxelizedMarksWithEnergy
- FromXmlList - Class in org.anchoranalysis.bean.define.adder
-
Adds a list of Named-Items define in a XML file in the current directory
- FromXmlList() - Constructor for class org.anchoranalysis.bean.define.adder.FromXmlList
- function(String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DescriptionMatch
- FunctionalIterate - Class in org.anchoranalysis.core.functional
-
Utilities for repeating operations a certain number of times.
- FunctionalList - Class in org.anchoranalysis.core.functional
-
Utilities functions for manipulating or creating
Listin a functional way - FunctionalProgress - Class in org.anchoranalysis.core.functional
-
Utilities for updating a
ProgressReporterin a functional way - functionAndType(String, String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DescriptionMatch
G
- GaussianBlur2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
- GaussianBlur2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
- GaussianFromParams - Class in org.anchoranalysis.plugin.image.feature.bean.score
- GaussianFromParams() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
- GaussianSamplerFromParams - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
- GaussianSamplerFromParams() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
- GaussianScore<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.score
- GaussianScore() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
- GaussianScoreCalculator - Class in org.anchoranalysis.plugin.operator.feature.score
-
Calculates a Gaussian Score
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in interface org.anchoranalysis.mpp.feature.addcriteria.AddCriteria
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
- generateEdge(VoxelizedMarkMemo, VoxelizedMarkMemo, EnergyStack, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
- generateIntersectingObjects(int, int, boolean) - Static method in class org.anchoranalysis.test.feature.plugins.objects.IntersectingCircleObjectsFixture
-
Generates a number of circles that intersect and don't intersect
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.KernelIterDescriptionSerializerPeriodicReporter
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFileMarksReporter
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
- generateIterableElement(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
- GenerateLabelHeadersForCSV - Class in org.anchoranalysis.plugin.image.task.feature
-
Generates a list of header-names for columns unrelated to features (identifiers and groups)
- GenerateLabelHeadersForCSV(String[], Optional<String>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.GenerateLabelHeadersForCSV
- generateNormal(double, double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
-
Generates a Gaussian (Normal) random variable with particular parameterization.
- generateNormal(double, double) - Method in class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
- generatePoisson(double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
-
Generates a Poisson random variable with particular parameterization.
- generatePoisson(double) - Method in class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
- generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.Mark
- generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
- generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
- generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
- generateProperties(Optional<Resolution>) - Method in class org.anchoranalysis.overlay.Overlay
- GenerateToMatchObjects - Class in org.anchoranalysis.plugin.image.bean.color.provider
-
Generates colors to match the size of an object-collection
- GenerateToMatchObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
- GenerateUniqueParameterization - Interface in org.anchoranalysis.bean
-
Objects that must implement well-defined
equals()andhashCode()methods and also generate a name uniquely identifying the class and all parameterization - Generator<T> - Interface in org.anchoranalysis.io.generator
-
A class that writes a particular type of object(s) to the filesystem.
- GeneratorBridge<S,T> - Class in org.anchoranalysis.io.generator
-
Exposes a
Generator<T>as if it was anGenerator<S>. - Geometry - Class in org.anchoranalysis.plugin.mpp.segment.bean.annealing
- Geometry() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
- Geometry(double, double) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
- get() - Method in class org.anchoranalysis.core.cache.CachedSupplier
- get() - Method in class org.anchoranalysis.core.concurrency.WithPriority
- get() - Method in interface org.anchoranalysis.core.functional.checked.CheckedSupplier
-
Applies a supplier like with
Supplier.get(). - get() - Method in interface org.anchoranalysis.core.identifier.provider.store.StoreSupplier
-
Gets the object being supplied to the store
- get() - Static method in class org.anchoranalysis.core.progress.ProgressReporterNull
- get() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
-
Returns the underlying feature-input (independent of the session)
- get() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
- get() - Method in interface org.anchoranalysis.feature.session.strategy.child.CacheSupplier
- get() - Method in class org.anchoranalysis.io.manifest.finder.FinderFileAsText
- get() - Method in class org.anchoranalysis.io.manifest.finder.FinderKeyValueParams
- get() - Method in class org.anchoranalysis.io.manifest.finder.FinderSerializedObject
- get() - Method in interface org.anchoranalysis.io.manifest.finder.SerializedObjectSupplier
- get() - Method in interface org.anchoranalysis.io.output.writer.ElementSupplier
-
Gets/creates the element to be written.
- get() - Method in interface org.anchoranalysis.io.output.writer.ElementWriterSupplier
-
Gets/creates the
ElementWriterto be used for an output. - get() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
- get() - Method in class org.anchoranalysis.plugin.io.manifest.DeserializedManifest
- get() - Method in interface org.anchoranalysis.plugin.operator.feature.score.FeatureResultSupplier
- get(int) - Method in interface org.anchoranalysis.core.color.ColorIndex
- get(int) - Method in class org.anchoranalysis.core.color.ColorIndexModulo
- get(int) - Method in class org.anchoranalysis.core.color.ColorList
- get(int) - Method in class org.anchoranalysis.core.color.SingleColor
- get(int) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
- get(int) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
- get(int) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
- get(int) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
- get(int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
- get(int) - Method in interface org.anchoranalysis.core.index.GetterFromIndex
- get(int) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- get(int) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
- get(int) - Method in class org.anchoranalysis.feature.name.FeatureNameList
- get(int) - Method in class org.anchoranalysis.feature.results.ResultsVector
- get(int) - Method in class org.anchoranalysis.feature.results.ResultsVectorList
- get(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
- get(int) - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
- get(int) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- get(int) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
- get(int) - Method in class org.anchoranalysis.image.core.stack.TimeSequence
- get(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- get(int) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
- get(int) - Method in interface org.anchoranalysis.io.bioformats.DestinationChannelForIndex
- get(int) - Method in class org.anchoranalysis.io.manifest.directory.sequenced.DeriveElementsFromSequencedDirectory
- get(int) - Method in class org.anchoranalysis.math.arithmetic.RunningSumCollection
-
An individual item in the collection.
- get(int) - Method in class org.anchoranalysis.math.moment.ImageMoments
- get(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
- get(int) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- get(int) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- get(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
- get(int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- get(int) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
- get(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
- get(int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
- get(int) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- get(int) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- get(int) - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
- get(int) - Method in class org.anchoranalysis.spatial.box.BoundedList
-
Gets a particular element
- get(int, int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
- get(Class<? extends T>) - Method in class org.anchoranalysis.bean.BeanInstanceMap
- get(String) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
- get(String) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
- get(String) - Method in interface org.anchoranalysis.mpp.io.input.MultiInputSubMap
-
Returns null if non-existent
- get(String) - Method in class org.anchoranalysis.mpp.io.input.OperationMap
- get(String) - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
- get(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels
- get(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.IndexedCSVRows
- get(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.MapGroupToRow
- get(Optional<String>) - Method in class org.anchoranalysis.io.output.outputter.InputOutputContextSubdirectoryCache
-
Gets (from the cache if it's already there) a context for a subdirectory of given-name
- get(K) - Method in class org.anchoranalysis.core.cache.LRUCache
- get(ProgressReporter) - Method in class org.anchoranalysis.core.progress.CachedProgressingSupplier
- get(ProgressReporter) - Method in interface org.anchoranalysis.core.progress.CheckedProgressingSupplier
- get(ProgressReporter) - Method in interface org.anchoranalysis.image.core.stack.NamedStacksSupplier
- get(VoxelDataType) - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataTypeFactoryMultiplexer
-
Multiplexes one of the factories according to data-type
- get(T) - Method in class org.anchoranalysis.image.experiment.label.FileLabelMap
- get(T, int) - Method in interface org.anchoranalysis.plot.GetForSeries
- getAboveMaxValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
-
Constant to return if outside the range (above the maximum allowed)
- getAcceptAll() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- getAdd() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
- getAddCriteria() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- getAdditionalBackgrounds() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
-
Additional background-stacks that are possible to use while annotating.
- getAdditionalChannels() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
-
Additional channels other than the main one, which are located in the main raster file
- getAdditionalChannels() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
Additional channels other than the main one, which are located in the main raster file
- getAdditionalPropertyPaths() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
-
Additional property paths that are also changed, along with the main propertyPath *
- getAddSum() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
-
Added to all gradients (so we can store negative gradients)
- getAdjacentChannels() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
Channels that are located in a separate raster file adjacent to the main raster file
- getAfterPreoperation() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
-
After pre-operation but before scaling
- getAggInterval() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
- getAggIntervalLog10() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
-
How many iterations before printing a new report? Encoded in log10.
- getAggregateReceiver() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
- getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
- getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
- getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
- getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
- getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
- getAggregateReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
- getAggregateTriggerBank() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- getAll() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
-
Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component
- getAllCacheNames() - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
- getAllKernelFactories() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- getAllowsChildren() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- getAngle() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
-
Angle part of axis-angle orientation (in radians)
- getAngleDegrees() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- getAngleDegrees() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
- getAngleRadians() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- getAnnealScheme() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
- getAnnotations() - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
- getAnnotatorStrategy() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
- getAppendChannels() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
Channels that are located in a separate raster file somewhere else in the project's structure
- getAppendCsv() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
- getAppendCSV() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
- getAppendHistogram() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- getAppendObjects() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
-
Appends object-collections to the multi-input
- getAppendStack() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- getArbitrary() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
- getArbitraryElement() - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider
-
Gets one element of the provider (arbitrarily)
- getArrange() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
- getArrange() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
- getAsBoolean() - Method in interface org.anchoranalysis.core.functional.checked.CheckedBooleanSupplier
-
Applies a supplier like with
BooleanSupplier.getAsBoolean(). - getAssigner() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- getAssignMode() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
- getAssociatedElementRange() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
- getAssociatedElementRange() - Method in interface org.anchoranalysis.io.manifest.directory.sequenced.SequencedDirectory
-
The associated element-range with ths folder.
- getAssociatedMark() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- getAsSupplier(String) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
- getAxis() - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
-
Which axis the unit-vector will align with.
- getAxis() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
-
Axis part of axis-angle orientation (should be normalized)
- getAxis() - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
- getAxis() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
-
Which axis? X=0, Y=1, Z=2
- getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
- getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
- getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
- getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
- getAxis() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
-
Which axis to read from (x,y,z)
- getAxis() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
- getAxisColor() - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- getAxisMax() - Method in class org.anchoranalysis.plot.AxisLimits
- getAxisMin() - Method in class org.anchoranalysis.plot.AxisLimits
- getBackground() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
- getBackground() - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
-
The background
- getBackground() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
-
The background.
- getBackgroundChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
-
Uses only this channel (identified by an index in the stack) as the background, -1 disables.
- getBackgroundChannelName() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- getBackgroundChannelProvider() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
- getBackgroundColor() - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- getBackgroundID() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
- getBackgroundStackMap() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
-
If non-null, maps underlying stack-name to a background
- getBackgroundStackName() - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
- getBeanExtension() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- getBeanExtension() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- getBeanName() - Method in class org.anchoranalysis.bean.AnchorBean
-
A short-name identifying a bean (by default the name of the class associated with the bean).
- getBelowMinValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
-
Constant to return if outside the range (below the minimum allowed)
- getBest() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
- getBest() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- getBestState() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- getBinaryInputChannelID() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
-
The ID of the binary input mask that determines the region of the watershed
- getBinarySgmn() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
- getBirthRepeats() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
- getBitsPerPixel() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
- getBlockSize() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
-
The block-size as per OpenCV implementation (identical default-size)
- getBlockStride() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
-
The block-stride as per OpenCV implementation (identical default-size)
- getBlue() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
- getBlue() - Method in class org.anchoranalysis.core.color.RGBColor
- getBlue() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
- getBorderWidth() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
-
Adds a border around each part of the montage
- getBoundCalculator() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
- getBoundCalculator() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
- getBoundRadius() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- getBounds() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
- getBoundsRatio() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
- getBoundType() - Method in class org.anchoranalysis.core.index.bounded.BoundChangeEvent
- getBridgeMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
-
Used to match each input-object to an intermediary-object
- getBundleSize() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
- getBundleSize() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- getCache() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
- getCache() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
- getCache() - Method in class org.anchoranalysis.feature.session.strategy.replace.CacheAndReuseStrategy
- getCacheNames() - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSource
- getCacheSize() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
-
Size of feature evaluation cache for featureEvaluatorMatch
- getCalculateLevel() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
- getCalculateLevel() - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
- getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
-
Method to calculate the level for a particular object.
- getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
-
Calculates the level for the threshold
- getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
- getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
- getCalculateLevel() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
- getCalculateLevelElse() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
- getCalculator() - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
- getCellDefault() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
- getCells() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
- getCellSize() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
-
The cell-size as per OpenCV implementation (identical default-size)
- getCenter() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
- getCenterPoint() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- getCenterPointX() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
- getCenterPointY() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
- getChangedMarkIDArr() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
- getChangedMarkIDs() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- getChannel() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
- getChannel() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
- getChannel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
- getChannel() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
- getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
- getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
- getChannel() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
- getChannel() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
-
A channel that is provided to the stack.
- getChannel() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
- getChannel(int) - Method in class org.anchoranalysis.feature.energy.EnergyStack
- getChannel(int) - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
- getChannel(int) - Method in class org.anchoranalysis.image.core.stack.Stack
- getChannel(int) - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
- getChannel(String) - Method in class org.anchoranalysis.plugin.image.task.channel.ChannelGetterForTimepoint
- getChannel1() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
- getChannel1() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
- getChannel2() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
- getChannel2() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
- getChannel3() - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
- getChannelAssignFrom() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
- getChannelChecker() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState
- getChannelConversionStyle() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
-
To convert as RGB or independently or in another way
- getChannelConverter() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
- getChannelConverter() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
-
Optionally, how to convert from one bit-depth to another (scaling, clipping etc.)
- getChannelElse() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
- getChannelFilter() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
-
Optionally, includes only certain channels when converting.
- getChannelFirst() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
-
Index of first channel
- getChannelGroupID() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- getChannelID() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
-
The ID of the channel that provides the input to the filter
- getChannelIfVoxelZero() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
-
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead
- getChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
- getChannelIndex() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
- getChannelIndex() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
- getChannelIndex() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
-
If either stackAsChannel==true or we have specified additionalChannels this indicated which channel to use from the stack
- getChannelLookup() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
- getChannelMap() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
- getChannelMask() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
-
If defined, this is the name of channel used as a mask over the values which are fed into the histogram
- getChannelName() - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
- getChannelName() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
-
By default all channels are converted into a stack.
- getChannelNum() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
- getChannelNum() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- getChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
- getChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
- getChannelSecond() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
-
Index of second channel
- getChannelsExtra() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- getChannelsPerByteArray() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceChannelsPerByteArray
- getChannelThreshold() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
- getChannelType() - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelChecker
- getChart() - Method in class org.anchoranalysis.plot.PlotInstance
- getCheck() - Method in class org.anchoranalysis.plugin.mpp.bean.check.Not
- getChecked() - Method in class org.anchoranalysis.io.output.outputter.Outputter
-
Gets the underlying delegate of
Outputterthat throws checked-exceptions instead of using aErrorReporter. - getCheckMark() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
- getCheckMark() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
- getCheckMark() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
- getCheckParsedFilePathBag() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
-
Imposes a condition on each parsedFilePathBag which must be-fulfilled if a file is to be included
- getChildAt(int) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- getChildCount() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- getClassifierProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
- getClassLoader() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
- getClassOfTarget() - Method in class org.anchoranalysis.bean.initializable.property.ExtractFromParam
- getCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
- getCol() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
- getCol(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
- getColForListIndex(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
- getCollection() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
- getCollectionID() - Method in class org.anchoranalysis.feature.bean.list.ParametersAsFeatures
- getCollectionID() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
- getColor() - Method in class org.anchoranalysis.bean.shared.color.scheme.FromSingle
-
The single color to repeat.
- getColor() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
-
An optional color associated with the label when displayed via GUI
- getColor() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
- getColor(int) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- getColorIDGetter() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
-
Gets a color ID associated with the object
- getColorIndex() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
-
Colors for a given index
- getColorList() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- getColorList() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- getColors() - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
-
The delegate that creates the (unshuffled) list.
- getColors() - Method in class org.anchoranalysis.bean.shared.color.scheme.FromList
-
The list of colors to specify
- getColors() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
-
Colors to use for drawing objects
- getColors() - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection
-
The colors in the collection.
- getColorScheme() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
- getColorsUnpaired() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- getColorUnselectedObjects() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
-
Optionally outline the other (unselected for the thumbnail) objects in this particular color.
- getColumnDefinition() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
-
Column definition for the CSVfiles
- getColumnFirstNumberPixels() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with the number of pixels for the first Object
- getColumnFirstPointX() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with X coordinate of point for the first Object
- getColumnFirstPointY() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with Y coordinate of point for the first Object
- getColumnFirstPointZ() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with Z coordinate of point for the first Object
- getColumnGroup() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
-
Name of CSV column used to group results (the same values, are outputted together)
- getColumnID() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
-
Name of CSV column with the file identifier
- getColumnNumPixels() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
-
Name of CSV column with the number of pixels for the first Object
- getColumnPointX() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
-
Name of CSV column with X coordinate of point for the first Object
- getColumnPointY() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
-
Name of CSV column with Y coordinate of point for the first Object
- getColumnPointZ() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
-
Name of CSV column with Z coordinate of point for the first Object
- getColumns() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
-
How many columns to use in the montage, or 0 to guess an approximately square output
- getColumnSecondNumberPixels() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with the number of pixels for the second Object
- getColumnSecondPointX() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with X coordinate of point for the first Object
- getColumnSecondPointY() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with Y coordinate of point for the first Object
- getColumnSecondPointZ() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with Z coordinate of point for the first Object
- getCombine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- getCombined() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
-
A path that combines the
directoryandfileNamePrefix. - getCombined() - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
- getCombined() - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
- getCommand() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
-
One of: open, close, fill, erode, dilate, skel, outline
- getCommandName() - Method in class org.anchoranalysis.launcher.config.HelpConfig
-
What the application command is described as in the help message e.g. anchor or anchorGUI
- getComparerLeft() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- getComparerMultiplex(boolean) - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
- getComparerRight() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- getComparers() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
- getCondition() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
- getCondition() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
- getConfidence() - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
- getConfidenceThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
-
The maximum difference in confidence for merging.
- getConfigDir() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
-
the directory where configuration files are stored
- getConnPoint() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
- getConstant() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
- getConstantBound() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
- getContains() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
- getContains() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
-
A descriptive-name must contain (case-sensitive) this string.
- getContext() - Method in class org.anchoranalysis.core.identifier.provider.store.SharedObjects
-
Logger and other common configuration
- getContext() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
- getContext() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
- getConvert() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
- getConverters() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- getCopyFilesMethod() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- getCopyFilesNaming() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
- getCopyFilesNaming() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- getCost() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeStrategy
- getCost(int, int) - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
-
Gets the cost from an element from the first-list to an element from the second-list.
- getCosts() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentObjectFactory
- getCount() - Method in class org.anchoranalysis.math.arithmetic.Counter
- getCount() - Method in class org.anchoranalysis.math.arithmetic.RunningSum
-
The running count
- getCount() - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
- getCount(int) - Method in class org.anchoranalysis.math.histogram.Histogram
- getCountThreshold() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
-
If there are more than
countThresholdelements, usesummarizerGreaterThan, elsesummarizerElse. - getCountXY() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
-
The count for XY dimensions (guaranteed to always be the same
- getCountZ() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
-
The count for Z dimension (this is identical to
RunningSumPoint.getCountXY()if only 3D points have ben added) - getCreateMark() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.PointsFitter
- getCsvFeaturesAggregated() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
-
The CSV of aggregated feature-results, if enabled.
- getCsvFeaturesGroup() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
-
The CSV individually written for each group, if enabled.
- getCsvFeaturesNonAggregated() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
-
The CSV of non-aggregated feature-results
- getCsvFilePath() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
- getCsvFilePath() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
- getCurrent() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
- getCurrent() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- getCurrentTemp() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
- getCustomName() - Method in class org.anchoranalysis.feature.bean.Feature
-
An optional additional name that be associated with the feature (defaults to an empty string)
- getDatasetName() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
The name of the experiment including version suffix
- getDatasets() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- getDatasets() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- getDatasetSpecific() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- getDatasetSpecific() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- getDatasetSuffix() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
-
A suffix appended to the dataset name extracted from the reg exp
- getDatasetVersion() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
A version-suffix appended to the dataset name extracted from the reg exp
- getDefault() - Static method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
-
Default values to use, if not otherwise specified
- getDefault() - Static method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
- getDefaultBeanClass() - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
-
Returns null as
Optionalis not supported byBeanFactoryinterface. - getDefaultColors() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
-
The default color-scheme used for outputs, if no other scheme is specified.
- getDefaultInstances() - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
- getDefaultInstances() - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories
- getDefine() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
- getDefine() - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
- getDefine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
-
Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
- getDefine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
- getDefine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- getDefine() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- getDefine() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Adds definitions of stacks/objects etc.
- getDelaySizeAtEnd() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
The underlying storage buffer, to which calls are delegated with our without conversion.
- getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
-
The underlying storage buffer, to which calls are delegated with our without conversion.
- getDelegate() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
The underlying storage buffer, to which calls are delegated with our without conversion.
- getDelegate() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
- getDelegate() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
- getDelimiter() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
- getDelta() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
- getDeltat() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
- getDepth() - Method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter.TraversalResult
- getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.AnnotationMarksComparer
- getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MarksComparer
- getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
- getDerivePath() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.ObjectComparer
- getDerivePath() - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.CollapseFileName
- getDerivePath() - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
- getDescription() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
- getDescription() - Method in class org.anchoranalysis.io.manifest.ManifestDirectoryDescription
- getDescription() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
- getDescription() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
- getDestination() - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
- getDestination() - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
- getDestination() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.DualVoxelizedMarks
- getDestination() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
- getDestinationFolderPath() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- getDimensions() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForMPP
- getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
- getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
- getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
-
Dimensions to create new mask
- getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
- getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
- getDimensions() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
- getDimensions() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
- getDimensions() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
- getDimensions() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
- getDimensionsOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
- getDimensionsRequired() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
- getDimensionsSource() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
- getDimensionsTarget() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
- getDirection() - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
-
Direction of the distance being converted, defaults to a unit vector along the X-axis
- getDirection() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
- getDirectionVector() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- getDirectionVector() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
- getDirectory() - Method in class org.anchoranalysis.core.system.path.PathDifference
-
The directory component of the difference, if it exists.
- getDirectory() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
-
The directory to which the output-manager is bound to.
- getDirectory() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
- getDirectory() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
-
A relative-path (to the user home directory) which is used as an output directory
- getDirectoryDistance() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
-
How many directories to recurse back from the current file to the Experiments/ directory
- getDistance() - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
- getDistance() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
-
How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
- getDistance() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
- getDistanceMapProvider() - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
-
A distance map which can also be used for making decisions on merging
- getDistanceMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
- getDistanceTransformMultiplyBy() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
-
Multiplies the distance transform by this factor to make it more meaningful in a short
- getDistanceTransformSmoothSigmaMeters() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
-
If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below
- getDistanceX() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
- getDistanceY() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
- getDistanceZ() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
- getDistanceZEndIfEmpty() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- getDivideByZeroValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
- getDivisor() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
-
Divide by
- getDivisor() - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
-
What the identifier is divided by to find the modulo.
- getDoubleOrNull(int) - Method in class org.anchoranalysis.feature.results.ResultsVector
- getDrawObject() - Method in class org.anchoranalysis.mpp.io.marks.generator.SimpleOverlayWriter
- getDrawObject() - Method in class org.anchoranalysis.overlay.writer.DrawOverlay
- getDscr() - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
- getDscr() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
- getDualStack() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
- getEigenvalue() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
- getEigenvector() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
- getElemAllAsFeatureList() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
- getElemAllCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- getElemByCliqueSize(int) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
- getElement() - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
- getElemIndAsFeatureList() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
- getElemIndCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- getElemPairAsFeatureList() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
- getElemPairCreator() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- getEllipseSum(double, double, DoubleMatrix2D) - Static method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- getEllipsoidCalculator() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- getEllipsoidSum(double, double, double, DoubleMatrix2D) - Static method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- getEmptyValue() - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
- getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
- getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
- getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
- getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
- getEmptyValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
- getEnd() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
-
An index beyond which we cannot iterate (inclusive)
- getEndPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- getEnergy() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
- getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
- getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
- getEnergyChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
- getEnergyChannelIndexCheck() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- getEnergyChannelIndexFail() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
-
Index of which channel in the energy-stack to select
- getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
-
Index of which channel in the energy-stack to select
- getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
-
Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
- getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
- getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
-
The channel that that forms the histogram
- getEnergyIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
-
The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions
- getEnergyIndex() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
- getEnergyIndexGradient() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
- getEnergyIndexMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
-
A channel of the energyStack that is used as an additional mask using default byte values for ON and OFF
- getEnergyIndexMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
-
Optionally, index of another channel that masks the histogram.
- getEnergyIndexX() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
- getEnergyIndexY() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
- getEnergyIndexZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
- getEnergyParamsName() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
-
If non-empty, A keyValueParams is treated as part of the energyStack
- getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
-
Associated Energy Scheme, which should include the EnergySavedPairs
- getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- getEnergyScheme() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
- getEnergyScheme() - Method in class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
- getEnergyScheme() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
- getEnergySchemeCreator() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
- getEnergySchemeCreator() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Creates an energy scheme that assigns an energy score to each collection of marks.
- getEnergyStack() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
- getEnergyStack() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
- getEnergyStack() - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
-
The energy-stack
- getEnergyStack() - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.FeatureCalculatorFromProvider
- getEnergyStack() - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
- getEnergyStackOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
-
Returns the energy-stack which may or not be present
- getEnergyStackRequired() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
-
Returns the energy-stack or throws an exception if it's not set as it's required.
- getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
- getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
-
The pre-annealed total energy
- getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
- getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- getEnergyTotal() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
-
Pairwise energy total
- getEquals() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
-
A descriptive-name must be exactly equal to (case-sensitive) this string.
- getErrorMessage() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- getErrorNode() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
- getErrorReporter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
-
The associated error reporter.
- getErrorReporter() - Method in class org.anchoranalysis.io.output.outputter.Outputter
- getErrorReporter() - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger
- getErrorTree() - Method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
- getExactDepth() - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
- getException() - Method in exception org.anchoranalysis.core.functional.CheckedStream.ConvertedToRuntimeException
- getException(int) - Method in class org.anchoranalysis.feature.results.ResultsVector
- getException(String) - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider
-
Retrieves the item if it exists, or throws an exception if it doesn't exist.
- getException(String) - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
- getException(String) - Method in class org.anchoranalysis.feature.shared.SharedFeatureSet
- getExecutionTime() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
- getExecutionTime() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- getExperimentalManifest() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
- getExperimentArguments() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
- getExperimentArguments() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
- getExperimentDescription() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
- getExperimentIdentifier() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
-
A name for the experiment.
- getExperimentIdentifier() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
- getExperimentIdentifier() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- getExperimentManifest() - Method in class org.anchoranalysis.plugin.io.manifest.CoupledManifests
- getExperimentType() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
-
A folder identifying the type of experiment (where the outputs are all put in the same directory
- getExperimentType() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
A folder identifying the type of experiment (where the outputs are all put in the same directory
- getExperimentType() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
- getExperimentType() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
-
The value of $1 (see comment above) in naming-structure.
- getExpression() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- getExtension() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
- getExtension() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
- getExtensionHTML() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
- getExtensionSerialized() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
- getExtensionText() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
- getExtensionXML() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
- getExtra() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
- getExtractScoreSize() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
- getExtractScoreSize() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
- getExtractScoreSizeReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- getExtractScoreSizeState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- getExtractWeight() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
- getFactor() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
- getFactor() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
- getFactorHigh() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
- getFactorLow() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
- getFactorStdDev() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
- getFallback() - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGB
-
If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
- getFallbackName() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
-
If there's no task-name, then this constant is used as a fallback name
- getFeature() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
-
The list feature that is duplicated, and populated.
- getFeature() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
- getFeature() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session
- getFeature() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- getFeature() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
-
Feature that calculates the score for an object.
- getFeature() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
- getFeature() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
- getFeature() - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- getFeature() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
- getFeatureCondition() - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
- getFeatureCondition() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
-
Calculates value for the condition - which is checked if it lies within a certain range
- getFeatureElse() - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
- getFeatureEvaluator() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
- getFeatureEvaluator() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
- getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
- getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
- getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
- getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
- getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
- getFeatureEvaluator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
- getFeatureEvaluatorMatch() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
- getFeatureEvaluatorMerge() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
- getFeatureEvaluatorThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
-
Allows merge only if the feature-value satisfies a relation to this threshold
- getFeatureListRef() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
- getFeatureListSet() - Method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
- getFeatureNameIndex() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
- getFeatureNames() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
- getFeatureNames() - Method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
- getFeatures() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator
-
A list of providers, combined together to form a list of features, to be calculated in a session
- getFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
-
The features to be exported (after possibly some manipulation or augmentation)
- getFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
-
Features to calculate for objects in the features output.
- getFeaturesAggregate() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
-
Features applied to each group to aggregate values (takes FeatureResultsVectorCollection)
- getFeaturesImage() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
-
Additional features that only depend on the image, so do not need to be replicated for every object.
- getFeaturesPair() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
-
Additional features that are processed on the pair of images (i.e.
- getFeatureTables() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
-
Specifies a feature-table that can also be outputted.
- getFeedbackReceiver() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
- getFeedbackReceiver() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Processes feedback from the segmentation algorithm for outputting / debugging.
- getFileExtension() - Method in class org.anchoranalysis.io.manifest.file.FileType
- getFileFilter() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
Files to search for
- getFileId() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendCsv
-
Unique identifier for the stack, object-mask-collection etc.
- getFileId() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManagerWithFileID
-
Unique identifier for the stack, object-mask-collection etc.
- getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
- getFileInput() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
- getFileInput() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
-
A string indicating the input file(s)
- getFilename() - Method in class org.anchoranalysis.core.system.path.PathDifference
-
The file-name component of the difference, if it exists.
- getFileName() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
- getFileName() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
- getFilenamePrefix() - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
- getFilenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
- getFilenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle
-
The filename to be written, including prefix, suffix, etc.
- getFilenameWithoutExtension() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
- getFilenameWithoutExtension(int) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
-
Like
IndexableOutputNameStyle.getFilenameWithoutExtension()but incorporates an integer index. - getFilenameWithoutExtension(String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
-
Like
IndexableOutputNameStyle.getFilenameWithoutExtension()but incorporates an string index. - getFilePath() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
- getFilePath() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
- getFilePath() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
- getFilePath() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
- getFilePathParser() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- getFilePathParser() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
- getFilePathPrefixer() - Method in class org.anchoranalysis.io.output.bean.OutputManager
-
Determines a prefix to use when outputting a file based upon an input-path.
- getFilePathPrefixer() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
- getFilePathPrefixer() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
- getFilePathProviderSVM() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
- getFilePrefix() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- getFiles() - Method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter.TraversalResult
- getFilesProvider() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- getFilesProvider() - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
-
The files to use as inputs.
- getFilesProvider() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
- getFilesProvider() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
A path to the main channel of each file
- getFilter() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
- getFilter() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
- getFilter() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
- getFilter() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
- getFilterFilesCsv() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
If set, a CSV is read with two columns: the names of images and a
- getFilterInitParams(Path) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
- getFindOutlinePixelAngle() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
- getFirst() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
- getFirst() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
- getFirst() - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
-
Output-names in the first-level.
- getFirst() - Method in class org.anchoranalysis.mpp.segment.transformer.Compose
-
First transformation from
StoU - getFirst() - Method in class org.anchoranalysis.overlay.writer.PrecalculationOverlay
- getFirst() - Method in class org.anchoranalysis.plugin.points.contour.ContourList
- getFirstArgument() - Method in class org.anchoranalysis.launcher.config.HelpConfig
-
What the application argument is described as in the help message e.g. experimentFile.xml
- getFirstBinaryValues() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- getFirstBinaryValuesByte() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- getFirstDimensions() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
- getFirstExtent() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
- getFirstPoint() - Method in class org.anchoranalysis.spatial.Contour
- getFlatBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
- getFloat() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
- getFolderDataset() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- getFolderOutput() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- getFolderPath() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
- getForAllSlices(int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
- getForceReader() - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
-
If non-empty forces usage of a particular bioformats plugin
- GetForSeries<T,S> - Interface in org.anchoranalysis.plot
- getForSlice(int, int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
- getForward() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
- getFoundDirectory() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
- getFoundFile() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleFile
- getFoundOrLog(String, Logger) - Method in interface org.anchoranalysis.annotation.io.image.findable.Findable
-
Returns the found object (or empty() if it's not found.....
- getFoundOrLog(String, Logger) - Method in class org.anchoranalysis.annotation.io.image.findable.Found
- getFoundOrLog(String, Logger) - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
- getFriendlyName() - Method in class org.anchoranalysis.feature.bean.Feature
- getFriendlyName() - Method in interface org.anchoranalysis.feature.calculate.InitializableFeature
-
A friendly name that can be displayed to user describing the Feature.
- getFrom() - Method in class org.anchoranalysis.core.graph.TypedEdge
-
The vertex the edge joins from.
- getFuncScore() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.AccptProbCalculator
- getFunction() - Method in class org.anchoranalysis.io.manifest.ManifestDescription
-
Identifies the function the entity plays.
- getGaussianSigmaMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
- getGenerator() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
-
The generator to be (repeatedly) used to write elements in the sequence.
- getGradient() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- getGraphColorScheme() - Method in class org.anchoranalysis.plot.index.PlotIndexBase
- getGrayscaleReconstruction() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
- getGreen() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
- getGreen() - Method in class org.anchoranalysis.core.color.RGBColor
- getGreen() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
- getGroup() - Method in class org.anchoranalysis.feature.io.csv.RowLabels
-
an identifier for a higher-level group which the row belongs to (foreign key)
- getGroup() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
-
Specifies a group for the label (similar labels that are displayed together)
- getGroup() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
-
If non-null this file-path is used to determine the group of the file If null, no group is included.
- getGroup() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
-
If defined, translates a file-path into a group.
- getGroup() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
- getGroup() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
- getGroupGeneratorName() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
- getGroupHeaders() - Method in class org.anchoranalysis.feature.io.results.LabelHeaders
-
Headers describing the non-feature columns outputted in the CSV related to identifying the group of a row
- getGroupMap() - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState
- getGroupNum() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
- getHeaders() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
-
Headers for the CSV file
- getHeight() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
- getHistogram() - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
- getHistogram() - Method in class org.anchoranalysis.image.feature.histogram.FeatureInputHistogram
- getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
-
If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).
- getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
-
An optional histogram of voxel intensity values which can be used by
segment - getHistogram() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
-
The histogram to plot.
- getHistogram() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult
- getHistogram() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
-
If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
- getHistogramChannelIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
- getHistogramIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- getHistogramsExtra() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- getHistogramsOutputEnabled() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
-
Deprecated.What's allowed or not when outputting histograms
- getHorizontalAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
- getId() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
- getId() - Method in class org.anchoranalysis.feature.bean.operator.Reference
- getId() - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
- getId() - Method in class org.anchoranalysis.feature.bean.results.StatisticForFeature
- getId() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
- getId() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
- getId() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
- getId() - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
- getId() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
- getId() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
- getId() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference
- getId() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
- getId() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
- getId() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
-
ID for the particular object-collection
- getId() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
-
Translates an input file name to a unique ID
- getId() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsReference
- getId() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
- getId() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
- getId() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
- getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
- getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
- getId() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
- getId() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
- getId() - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
- getIdentifier() - Method in class org.anchoranalysis.mpp.mark.Mark
- getIdentifier() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
- getIdentifier() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
- getIdentifier() - Method in interface org.anchoranalysis.overlay.identifier.Identifiable
- getIdentifier() - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
- getIdentifier(ObjectWithProperties, int) - Method in class org.anchoranalysis.image.core.object.properties.IdentifierByProperty
- getIdentifier(ObjectWithProperties, int) - Method in class org.anchoranalysis.overlay.identifier.IdentifyDelegateToOverlays
- getIdentifier(Mark, int) - Method in class org.anchoranalysis.mpp.mark.IdentifierFromMark
- getIdentifier(Overlay, int) - Method in class org.anchoranalysis.overlay.identifier.IdentifierFromOverlay
- getIdentifier(T, int) - Method in interface org.anchoranalysis.core.identifier.getter.IdentifierGetter
- getIdentifier(T, int) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
- getIdentifier(T, int) - Method in class org.anchoranalysis.core.identifier.getter.IdentifyByIteration
- getIdentifierSuffix() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- getIdentifierSuffix() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- getIdGenerator() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
- getIdGetter() - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
- getIdGetter() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
-
Gets a unique ID associated with the object
- getIfPresent(K) - Method in class org.anchoranalysis.core.cache.LRUCache
-
Gets an value if present, but doesn't create any new entry if it's absent.
- getIgnoreContains() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
-
If non-empty any stackNames (after map) containing a certain string will be ignored
- getImage() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
- getImage() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- getImage() - Method in class org.anchoranalysis.mpp.bean.init.PointsInitParams
- getImageDimensions() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
- getImageInit() - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
- getImageLabeller() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
-
Maps a label to an image
- getImgChannelMapCreator() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- getIncrement() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
-
Size of step to use when incrementing
- getIncrementDegrees() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
- getIncrementDegrees() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
- getIndex() - Method in class org.anchoranalysis.core.index.Indexable
- getIndex() - Method in interface org.anchoranalysis.core.index.IndexGetter
- getIndex() - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
- getIndex() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
- getIndex() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
- getIndex() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
- getIndex() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
-
Index in z-dimension of slice to extract
- getIndex() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
-
Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)
- getIndex() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- getIndex() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.OrderedRadius
- getIndex() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
- getIndex() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
-
Which index to return from the HOG descriptor
- getIndex(String) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
- getIndex(TreeNode) - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- getIndexedRowsOrCreate(Path, ColumnDefinition) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVSharedState
- getIndexForMemo(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
- getIndexNonZero() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
- getIndividual() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- getInitContext() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- getInitializationParameters() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
- getInitialKernel() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- getInitialPoint() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
- getInitParams() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
- getInitParamType() - Method in class org.anchoranalysis.bean.initializable.property.PropertyInitializer
- getInnerCoreDistance() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- getInPathPrefix() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
- getInput() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
- getInput() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
-
The input-manager to specify where/which/how necessary inputs for the experiment occur.
- getInput() - Method in class org.anchoranalysis.experiment.task.InputBound
- getInput() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
- getInput() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
- getInput() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- getInput() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- getInput() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
- getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
- getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
- getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
- getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
- getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
- getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
- getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.Shuffle
- getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
- getInput() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
- getInput() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
- getInputDebug() - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
- getInputDirectory() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
-
A directory indicating where inputs can be located
- getInputFilterExtensions() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
-
If defined, a set of extension filters that can be applied on inputDirectory
- getInputIfPresent(T) - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSource
- getInputName() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- getInputName() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- getInputName() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
- getInputOutputContext() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
- getInputPaths() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
- getInputPointShift() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
- getInstance() - Static method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorFactory
- getInt(int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
-
Gets an element from the buffer at a particular position, converting, if necessary, to an
int. - getInt(int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
- getInt(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
- getIntensity() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- getIntensityHistogram() - Method in class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
- getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
- getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
-
Interpolator used when scaling the background
- getInterpolator() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
- getItem() - Method in class org.anchoranalysis.bean.NamedBean
-
The item that is to be named (i.e.
- getItem() - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
- getItem() - Method in class org.anchoranalysis.feature.bean.list.DefineSingle
- getItem() - Method in class org.anchoranalysis.feature.bean.list.PrependName
- getItem() - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
- getItem() - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
- getItem() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
- getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
- getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
- getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
-
For each feature in the list, a corresponding "aggregate" feature is created in the output list
- getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
-
Feature to apply to the histogram
- getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
- getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
- getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
- getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
- getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
- getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
-
Feature to apply to the histogram
- getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
- getItem() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
- getItem() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
- getItem() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CoefficientOfVarianceFromAll
- getItem() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MeanFromAll
- getItem() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
-
Feature to apply to the histogram
- getItem() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoOne
- getItem1() - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
- getItem2() - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
- getItemMean() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
- getItemProportionate() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeatureAsIndividualProportionate
- getItemStdDev() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
- getIteration() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- getIterations() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
- getIterations() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
- getIterations() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
- getIterations() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
-
The maximum number of iterations.
- getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
-
The number of dilations and erosions to apply to determine if two objects intersect
- getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
-
The number of dilations and erosions to apply and whether to do in the Z dimension
- getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
- getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
- getIterations() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
-
The number of dilations and erosions to apply and whether to do in the Z dimension
- getIterations() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
-
iterations for erode, dilate, open, close
- getIterations() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
- getIterationsDilation() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
-
Number of times to perform morphological dilation
- getIterationsErosion() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
-
Number of times to perform morphological erosion
- getJobDescription() - Method in class org.anchoranalysis.experiment.task.processor.SubmittedJob
- getJobManifest() - Method in class org.anchoranalysis.plugin.io.manifest.CoupledManifests
- getJobNumber() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
- getJobShortName() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
- getJobState() - Method in class org.anchoranalysis.experiment.task.processor.SubmittedJob
- getKappa() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
- getKeep() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
- getKeepProcessorsFree() - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
-
How many processors to avoid using for the tasks.
- getKeepProcessorsFree() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
-
How many processors to avoid using for the tasks.
- getKernel() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
- getKernel() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
- getKernel() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- getKernel() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- getKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
- getKernelAccepted() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- getKernelCalcContext() - Method in class org.anchoranalysis.mpp.segment.transformer.TransformationContext
- getKernelFactoryList() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- getKernelHalfWidth() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
-
Kernel will be a square kernel of size
(2*kernelHalfWidth+1)x(2*kernelHalfWidth+1) - getKernelNegative() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
- getKernelNoProposalDescription() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- getKernelPositive() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
- getKernelProposed() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- getKernelProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Proposes kernel-changes during iterations of hte marked-point-processes.
- getKernelStateBridge() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- getKey() - Method in exception org.anchoranalysis.core.index.GetOperationFailedException
- getKey() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
- getKey() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
- getKey() - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
- getKey() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
- getKey() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
- getKey() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- getKey() - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
- getKeyGroupID() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- getKeyLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
- getKeyMean() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
- getKeyPrefix() - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
-
Prefix prepended to key
- getKeyStdDev() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
- getKeySuffix() - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
- getKeyUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
- getKeyValueParams() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
- getKeyValueParamsID() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
- getKeyValueParamsID() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
-
If non-empty, the identifier of a key-value-params collection that is passed to the segmentation procedure.
- getLabel() - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
-
The label that applies to the image
- getLabelMap() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
- getLabels() - Method in class org.anchoranalysis.plot.index.PlotIndexBase
- getLabels() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
- getLast() - Method in class org.anchoranalysis.plugin.points.contour.ContourList
- getLastDivider() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- getLastPoint() - Method in class org.anchoranalysis.spatial.Contour
- getLastPoints1() - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
- getLastPoints2() - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
- getLeafDirectories() - Method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter.TraversalResult
- getLeft() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
-
Objects on left-side of the comparison
- getLevel() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
- getLevel() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult
- getLine() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
- getList() - Method in class org.anchoranalysis.bean.define.adder.Concatenate
- getList() - Method in class org.anchoranalysis.bean.shared.regex.RegExList
- getList() - Method in class org.anchoranalysis.bean.shared.StringMap
- getList() - Method in class org.anchoranalysis.experiment.bean.log.ToMultiple
-
The list of loggers to log to
- getList() - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
- getList() - Method in class org.anchoranalysis.feature.bean.list.Define
- getList() - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed
- getList() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- getList() - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
- getList() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
- getList() - Method in class org.anchoranalysis.io.manifest.finder.FinderExperimentFileDirectories
- getList() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
- getList() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
- getList() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
- getList() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
- getList() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
- getList() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
- getList() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine
-
A list of other filters from which the sub-classes implement filtering behaviour.
- getList() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
- getList() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
-
A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)
- getList() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
- getList() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
- getList() - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
- getList() - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate
- getList() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Combine
- getList() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
- getList() - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
- getList() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
- getList() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
- getList() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
- getList(Class<?>) - Method in class org.anchoranalysis.bean.define.Define
- getListAdditionalChannelProviders() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
- getListAppend() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- getListAppend() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
-
Additional entities that are appended to the multi-input
- getListAppendFilePath() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- getListAppendKeyValueParams() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- getListAppendMarks() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- getListAppendMarksFromAnnotation() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- getListAppendMarksFromAnnotationAcceptedOnly() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- getListAppendMarksFromAnnotationRejectedOnly() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- getListComparers() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
- getListFeatures() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
- getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendFilePath
- getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
- getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
- getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendMarks
- getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendObjects
- getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
- getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
- getListFromManager(MultiInputManager) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManager
- getListImageFeatures() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- getListImageFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
- getListPaired(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
- getListPaired(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
- getListPaired(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- getListReportFeatures() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
- getListReportFeatures() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
- getListStackProvider() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- getListStackProviderMIP() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- getListUnassigned(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
- getListUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
- getListUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- getListUnassignedLeft() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- getListUnassignedRight() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- getLocal(int) - Method in class org.anchoranalysis.image.voxel.kernel.LocalSlices
- getLocalPath() - Method in class org.anchoranalysis.bean.AnchorBean
-
A local path on the filesystem associated with this bean (from serialization) if defined.
- getLog() - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf
-
The logger to use if conditions are fulfilled
- getLog() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- getLogExperiment() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
-
Where log messages that do not pertain to a specific job (input) appear.
- getLogExperimentPath() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
-
Relative path to a logger for the experiment in gneeral
- getLogger() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
-
The logger
- getLogger() - Method in class org.anchoranalysis.core.log.CommonContext
-
The logger
- getLogger() - Method in class org.anchoranalysis.experiment.task.InputBound
- getLogger() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
- getLogger() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
-
The associated logger.
- getLogger() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
- getLogger() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
- getLogger() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
- getLogger() - Method in class org.anchoranalysis.mpp.segment.transformer.TransformationContext
- getLogger() - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects
- getLogger() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
- getLoggerExperiment() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
- getLoggerTaskCreator() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
- getLogReporterJob() - Method in class org.anchoranalysis.experiment.task.InputBound
- getLogTask() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
-
Where log messages that do pertain to a specific job (input) appear.
- getLogTaskPath() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
-
Relative path to a logger for a specific task
- getLookup() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
- getMainChannelIndex() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
Index of the mainChannel
- getMainChannelName() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
The name of the channel provided by the rasters in file Provider
- getMainObjectName() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- getMainObjectName() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
- getMajorAxisAngle() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
- getMajorAxisSlope() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
- getManifest() - Method in class org.anchoranalysis.experiment.task.InputBound
- getManifestDescription() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
-
A manifest-description for the directory, if defined.
- getManifestDescription() - Method in class org.anchoranalysis.io.manifest.file.FileType
- getManifestDescriptionFunction() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
- getManifestDeserializer() - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
- getManifestExperimentInputFileSet() - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
- getManifestFunction() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
- getManifestFunction() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- getManifestInputFileSet() - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
- getMap() - Method in class org.anchoranalysis.mpp.io.input.OperationMap
- getMap() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
- getMap() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
- getMark() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
- getMark() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
-
The associated mark
- getMark() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
- getMark() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
- getMark() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
- getMarkBounds() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
-
Backwards compatible for when we only had a single bounds
- getMarkBounds() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
- getMarkBounds() - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
- getMarkBoundsSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- getMarkEvaluator() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
-
A mark-evaluator that is added to the GUI to support this annotation
- getMarkFactory() - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
- getMarkFactory() - Method in class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
- getMarkFactory() - Method in class org.anchoranalysis.mpp.segment.kernel.MarkFactoryContext
- getMarkFactory() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
- getMarkFactory() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Creates a new mark, before perhaps further manipulations by a kernel.
- getMarkFactory() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
- getMarkFromMarksProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
- getMarkMergeProposerSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- getMarkProposer() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
-
Name of the
MarkProposerto use. - getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
- getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
- getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
- getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
- getMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
- getMarkProposerAdditionalBirth() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- getMarkProposerSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- getMarkProvider() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
- getMarkProvider() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
- getMarkProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
- getMarkProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
- getMarkProvider() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- getMarkRmv() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
- getMarks() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- getMarks() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
- getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
- getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
-
The marks
- getMarks() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- getMarks() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
- getMarks() - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
- getMarks() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- getMarks() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
- getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
- getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RetrieveSingleMarkOnly
- getMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
- getMarks() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.MarksFromPartition
- getMarksAfter() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- getMarksAfterOptional() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- getMarksCollection() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- getMarksColored() - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
- getMarksOutputEnabled() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
-
Deprecated.What's allowed or not when outputting configurations
- getMarkSplitProposerSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- getMarksProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
- getMarksProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
- getMarksProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
- getMarksProposerSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- getMarksReject() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
-
Marks covering area that should be rejected, can be null
- getMarksWithTotalEnergy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- getMask() - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
- getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
- getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
- getMask() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- getMask() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
- getMask() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
-
An optional mask which restricts the algorithm to only parts of the channel where the mask has an ON voxel
- getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
- getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
- getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
- getMask() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
- getMask() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
- getMask() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
-
A mask that is provided to the stack.
- getMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
- getMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
- getMask() - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
- getMask() - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
- getMask() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
- getMask() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- getMaskElse() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
-
Returned instead of
maskif the predicate is not satisfied - getMaskFilled() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
- getMaskFilled() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- getMaskIndex() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
- getMaskOutline() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
- getMaskValue() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
-
What voxel value to read as "On" in the mask above.
- getMaskValue() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
- getMatch() - Method in class org.anchoranalysis.feature.bean.list.SelectFromShared
- getMatch() - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
- getMatch() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
- getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
- getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
- getMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
- getMatches() - Method in class org.anchoranalysis.image.core.object.MatchedObject
-
The matches associated with the source-object
- getMatchString() - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
- getMatrix() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
-
A two-dimensional array mapping the costs from
firsttosecond - getMatrix() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
- getMavenProperties() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
- getMax() - Method in interface org.anchoranalysis.core.progress.ProgressReporter
- getMax() - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
- getMax() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
- getMax() - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
- getMax() - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
- getMax() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
- getMax() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
- getMax() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
- getMax() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
- getMax() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
- getMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
-
Maximum-boundary for acceptable range
- getMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
- getMax() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
- getMax() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
- getMax() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
-
Calculates maximally-allowed range boundary
- getMax() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
-
Boundary value indicating maximally-allowed range value
- getMaxBin() - Method in class org.anchoranalysis.math.histogram.Histogram
-
Maximum bin-value inclusive
- getMaxCost() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
- getMaxCost() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
- getMaxDirectoryDepth() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
- getMaxDistance() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
-
An optional maximum distance
- getMaxDistance() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
- getMaxDistance() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
- getMaxDistanceBetweenMinima() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
- getMaxDistanceCOG() - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
-
The maximum distance allowed between center-of-gravities of objects
- getMaxDistanceDeltaContour() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
-
The maximum distance allowed between two seeds in terms of their values in the distance map
- getMaxDistanceDeltaContour() - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
-
The maximum distance allowed between the 'distance from contour' values provided from the distanceMap for each point.
- getMaxDistanceProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
- getMaxDistanceZ() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
- getMaximumIndex() - Method in interface org.anchoranalysis.core.index.bounded.BoundedRange
- getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
- getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
- getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
- getMaximumIndex() - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
- getMaxIter() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Repeat
- getMaxIter() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Repeat
- getMaxIter() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
- getMaxIter() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
- getMaxNumber() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
- getMaxNumberItems() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Limit
- getMaxNumberProcessors() - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
-
An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
- getMaxNumberProcessors() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
-
Theoretical maximum number of (CPU) processors to use in parallel.
- getMaxNumberProcessors() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
-
An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
- getMaxNumberProcessors() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- getMaxNumItems() - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
- getMaxNumItems() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.LimitWithDirectory
- getMaxOfMax() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
- getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
- getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
- getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
- getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds
- getMaxResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
- getMaxSize() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
- getMaxSplitGroups() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- getMaxValue() - Method in class org.anchoranalysis.plugin.image.task.grouped.ConsistentChannelChecker
- getMaxVar() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
- getMaxVolume() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
- getMaxX() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
-
Maximum X coordinate inclusive
- getMaxY() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
-
Maximum Y coordinate inclusive
- getMaxZ() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
-
Maximum Z coordinate inclusive
- getMean() - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
-
Mean
- getMean(int) - Method in class org.anchoranalysis.math.moment.ImageMoments
-
Index is the axis (0 for X, 1 for Y, 2 for Z)
- getMedianRadiusMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
- getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
- getMemoForIndex(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
- getMemoForIndex(int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.memo.MemoForIndex
- getMemoForMark(Mark) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- getMemoForMark(MarkCollection, Mark) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
- getMemoized() - Method in class org.anchoranalysis.io.manifest.finder.FinderSerializedObject
-
Provides a memoized (cached) means of access the results of the finder
- getMerge() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
- getMerged() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
-
Returns a merged version of the two-objects available (or null if not available)
- getMergedOptional() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
- getMergedPosTolerance() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
- getMergeMarkProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- getMessage() - Method in exception org.anchoranalysis.core.index.GetOperationFailedException
- getMessage() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
- getMessageLogger() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
- getMessageReporter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
-
The associated message reporter.
- getMethod() - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
- getMethod() - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
-
One of the following strings to identify ImageJ's thresholding algorithms (or an empty string for the default).
- getMiddlePoint() - Method in class org.anchoranalysis.spatial.Contour
- getMin() - Method in interface org.anchoranalysis.core.progress.ProgressReporter
- getMin() - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
- getMin() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
- getMin() - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
- getMin() - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
- getMin() - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
- getMin() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
- getMin() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
- getMin() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
- getMin() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
-
Minimum-boundary for acceptable range
- getMin() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
- getMin() - Method in class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
- getMin() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
-
Calculates minimally-allowed range boundary
- getMin() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
-
Boundary value indicating minimally-allowed range value
- getMin(Function<FileDetails, Optional<Integer>>) - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
- getMinConfidence() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
-
The minimum confidence of an element for its object-mask to be included.
- getMinConfidence() - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
-
Proposed bounding boxes below this confidence interval are removed
- getMinDiff() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
- getMinDifference() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
-
A minimum difference, below which 0.0 is returned
- getMinDifference() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
- getMinDiversity() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
- getMinimaImposition() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
- getMinimumBoundingBoxVolume() - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
-
Only objects whose bounding-box volume is greater or equal to this threshold are included.
- getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
- getMinimumIndex() - Method in interface org.anchoranalysis.core.index.bounded.BoundedRange
- getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
- getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
- getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
- getMinimumIndex() - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
- getMinIntensity() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
- getMinIntensity() - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
-
Intensity for thresholding
- getMinIntensityValue() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
- getMinMaxIgnoreBeforeIndex() - Method in class org.anchoranalysis.plot.index.LinePlot
- getMinNumberObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- getMinNumberPoints() - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
-
If a contour has less than this number of points, we don't split it, and return it as-is
- getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
-
Only includes squares that have at lesat this number of voxels
- getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
- getMinNumberVoxels() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
-
The minimum number of voxels that must exist in a connected-component to be included.
- getMinNumPoints() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
- getMinNumPoints() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
-
If an object has fewer points than before being fitted, we ignore
- getMinNumSlices() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- getMinNumZSlices() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.check.AtLeastZSlices
- getMinorAxisAngle() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
- getMinorAxisSlope() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
- getMinOverlap() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
- getMinRadius() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
- getMinRadius() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
- getMinRadScaleEnd() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
- getMinRadScaleStart() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
- getMinRatio() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- getMinRatioPointsInsideRegion() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundDegrees
- getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundPhysicalExtent
- getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
- getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.MarkBounds
- getMinResolved(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
- getMinSize() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
- getMinusOne() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
- getMinVal() - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- getMinVolume() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
- getMinVolume() - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
- getMinVolumeConnectedComponent() - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
- getMinX() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
-
Minimum X coordinate inclusive
- getMinXYRes() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorMinXYRes
- getMinY() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
-
Minimum Y coordinate inclusive
- getMinZ() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
-
Minimum Z coordinate inclusive
- getModelDirectory() - Method in class org.anchoranalysis.core.log.CommonContext
-
Directory where machine-learning models can be found
- getModelDirectory() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
- getModelDirectory() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
- getModelDirectory() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- getModelDirectory() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
-
An input-directory in which models are stored.
- getModelDirectory() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
- getModelPool() - Method in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
- getMultipleComparer() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
- getMultiplyBy() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
- getName() - Method in class org.anchoranalysis.bean.define.adder.FromXmlList
-
The name of the file in the current working directory WITHOUT THE .xml EXTENSION
- getName() - Method in class org.anchoranalysis.bean.NamedBean
-
The name associated with
item - getName() - Method in class org.anchoranalysis.bean.shared.path.RootPath
- getName() - Method in interface org.anchoranalysis.core.identifier.name.NameValue
-
The associated name
- getName() - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
- getName() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
- getName() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
-
An optional-name.
- getName() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
- getName() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
- getName() - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
- getName() - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
- getName() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
-
A unique name associated with the path
- getName() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
- getName() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- getName() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- getName() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
- getName() - Method in class org.anchoranalysis.mpp.mark.Mark
- getName() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- getName() - Method in class org.anchoranalysis.mpp.mark.points.PointList
- getName() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
- getName() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
- getName() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
- getName() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
- getName() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
- getName() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
- getName() - Method in class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile
-
A name to describe the adjacent file
- getName() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
-
The name of the appended entity
- getName(S) - Method in interface org.anchoranalysis.bean.permute.ApplyPermutations.NameGetter
- getNamedFilePathCollection() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsInitParams
- getNamedKeyValueParamsCollection() - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsInitParams
- getNameLeft() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- getNamer() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
- getNamer() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- getNamer() - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
- getNamer() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
Assigns each input a unique compact name.
- getNameRight() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- getNames() - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
- getNames() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
- getNameValueSet() - Method in class org.anchoranalysis.overlay.OverlayProperties
- getNavigateHigherDirs() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
-
Search x number directories higher than file
- getNoProposalReason() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
- getNumberChannels() - Method in class org.anchoranalysis.feature.energy.EnergyStackWithoutParams
- getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.Stack
- getNumberChannels() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
- getNumberChannels() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
- getNumberChannels() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
- getNumberColors() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
- getNumberDilations() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
- getNumberElements() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
- getNumberElements() - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
- getNumberElements() - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
- getNumberElements() - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
- getNumberFrames() - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
- getNumberFrames() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
- getNumberGPUProcessors() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
-
How many GPU processors to use when this is possible as a substitute for a CPU processor
- getNumberKernels() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- getNumberLoopPoints() - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
- getNumberPoints() - Method in class org.anchoranalysis.plot.index.LinePlot
- getNumberSeries() - Method in class org.anchoranalysis.plot.index.PlotIndexBase
- getNumberSlices() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
- getNumberSubdirectories() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
-
How many directories to include in the name.
- getNumBins() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
-
The number of bins in each histogram for a cell
- getNumCols() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
- getNumColsUsed() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
- getNumDecimalPlaces() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
- getNumDim() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
- getNumLeadingZeros() - Method in class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
- getNumLevelsGrouping() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- getNumMarks() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
- getNumRep() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
- getNumRep() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingNumberMarks
- getNumRows() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
- getNumRowsUsed() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
- getObject() - Method in class org.anchoranalysis.annotation.io.image.findable.Found
-
The found object
- getObject() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
- getObject() - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
- getObject() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResult
- getObject() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
- getObject() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
- getObject1() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
- getObject2() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
- getObjectMatcher() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
-
Used to match each intermediary-object to a final-object
- getObjects() - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
- getObjects() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
- getObjects() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
- getObjects() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
- getObjects() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
-
The objects for whom a level is calculated
- getObjects() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
- getObjects() - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
- getObjects() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
- getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
- getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
- getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection
- getObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
- getObjects() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
-
Objects to draw on a background
- getObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
- getObjects() - Method in class org.anchoranalysis.plugin.image.object.ColoredObjectCollection
-
The objects in the collection.
- getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
- getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
- getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
- getObjects() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
- getObjects() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- getObjects() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
- getObjects() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
-
Deprecated.What's allowed or not when outputting object-collections
- getObjects() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
- getObjects() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- getObjects1() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
-
First collection with items to be merged
- getObjects2() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
-
Second collection with items to be merged
- getObjectsBlue() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
- getObjectsContainer() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
- getObjectsElse() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
- getObjectsGreater() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
- getObjectsGreen() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
- getObjectsGrouped() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
- getObjectsLesser() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
- getObjectsRed() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
- getObjectsRejected() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
- getObjectsSave() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
-
Saves all objects that are inputs to the merge, outputs from the merge, or intermediate merges along the way
- getObjectsSeeds() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
- getObjectsSeeds() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
- getObjectsSource() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
- getObjectsSource() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
- getObjectsSplitBy() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
- getObjectsTarget() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
- getOffByte() - Method in class org.anchoranalysis.image.core.mask.Mask
- getOffByte() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
-
The byte representation of the value for OFF
- getOffInt() - Method in class org.anchoranalysis.image.core.mask.Mask
- getOffInt() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
-
The integer representation of the value for OFF
- getOnByte() - Method in class org.anchoranalysis.image.core.mask.Mask
- getOnByte() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
-
The byte representation of the value for ON
- getOnInt() - Method in class org.anchoranalysis.image.core.mask.Mask
- getOnInt() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
-
The integer representation of the value for ON
- GetOperationFailedException - Exception in org.anchoranalysis.core.index
-
When a get operation fails for a particular key
- GetOperationFailedException(int, String) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
- GetOperationFailedException(int, Throwable) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
- GetOperationFailedException(Exception) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
- GetOperationFailedException(String, String) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
- GetOperationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.index.GetOperationFailedException
- getOptimization() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
The optimization-scheme that determines which configurations are accepted/rejected from one iteration to the next.
- getOptional(String) - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider
-
Retrieves the item if it exists, or returns empty() if it doesn't exist.
- getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
- getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
- getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
- getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
- getOptional(String) - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
- getOptional(String) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
- getOptional(String) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
- getOptional(String) - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequence
- getOptional(String) - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
- getOptional(String) - Method in class org.anchoranalysis.image.core.stack.wrap.WrapTimeSequenceAsStack
- getOptionList() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- getOptions() - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
- getOptions() - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
- getOrCalculate(T) - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculation
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
- getOrCalculate(T) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
- getOrCalculate(T, U) - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculationMap
- getOrCalculate(T, U) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
-
Executes the operation and returns a result, either by doing the calculation, or retrieving a cached-result from previously.
- getOrCreate(Class<?>) - Method in class org.anchoranalysis.core.identifier.provider.store.SharedObjects
-
Gets an existing store, or creates a new one
- getOrCreateNew(K) - Method in class org.anchoranalysis.core.identifier.name.MapCreate
- getOrientation() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- getOrientation() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- getOrientationProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
- getOrientationXYProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- getOriginal() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
-
Original unscaled element before any operations
- getOrNull(U) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
-
Gets an existing result for the current params from the cache.
- getOutlineColor() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
-
The color of the outline
- getOutlinePixelsRetriever() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
- getOutlinePixelsRetrieverReverse() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
- getOutlineProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
- getOutlineWidth() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
- getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
-
The width of the outline (only relevant if
outline==true - getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
-
The width of the outline.
- getOutlineWidth() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
-
The width of the outline
- getOutlineWidth() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
- getOutlineWidth() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- getOutPath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
-
Constructs a path as an output, replacing $1, $2 etc.
- getOutPathPrefix() - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
-
A directory in which to output the experiment-directory and files
- getOutput() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
-
The output-manager that specifies how/where/which elements occur duing outputting.
- getOutput() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
- getOutput() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- getOutputDirectory() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
-
A directory indicating where inputs can be located
- getOutputDirectory() - Method in class org.anchoranalysis.io.output.path.prefixer.FilePathPrefixerContext
-
A directory indicating where inputs can be located
- getOutputEnabled() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
-
Deprecated.What's allowed or not - highest level outputs
- getOutputEnabled() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- getOutputEnabledDelta() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
-
Additions/subtractions of outputs for the experiment supplied by the user.
- getOutputFolderPath() - Method in class org.anchoranalysis.io.output.outputter.Outputter
- getOutputFolderPath() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
- getOutputName() - Method in class org.anchoranalysis.experiment.bean.log.ToTextFileBase
-
The name to use (without extension) for the text-file log
- getOutputName() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
-
The output name for the features CSV.
- getOutputName() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
- getOutputName() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
- getOutputName() - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle
-
An identifier used in rules to determine if an output is enabled or not.
- getOutputName() - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
- getOutputName() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
- getOutputName() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
- getOutputName() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- getOutputNameStyle() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
- getOutputNameStyle() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.FromOutputName
- getOutputPattern() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
- getOutputRGBOutline() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- getOutputRGBOutlineFlattened() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- getOutputsDisabled() - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
-
The names of the outputs that are disbled.
- getOutputsEnabled() - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
-
The names of the outputs that are enabled.
- getOutputsEnabled() - Method in class org.anchoranalysis.io.output.bean.OutputManager
-
Which outputs are enabled or not enabled.
- getOutputsEnabled() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
-
Which outputs are enabled or not enabled.
- getOutputStackProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
-
If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
- getOutputter() - Method in class org.anchoranalysis.experiment.task.InputBound
- getOutputter() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
- getOutputter() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
- getOutputter() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
-
The outputter to be used for the sequence.
- getOutputter() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
-
An outputter that writes to the particular output-directory.
- getOutputter() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
- getOutputterFor(String) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
-
groupIdentifierFor should always called at least once before getOutputManagerFor
- getOutputWriteSettings() - Method in class org.anchoranalysis.io.output.bean.OutputManager
-
General settings (default file extensions, colors etc.) for outtping files.
- getOutputWriteSettings() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- getOutside() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
-
Returned as a constant if a value lies otside the range
- getOverlapRatioThreshold() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- getOverlapThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
-
The maximum size for merging.
- getOverlays() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- getOverlays() - Method in class org.anchoranalysis.overlay.IndexableOverlays
- getPadding() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
-
Padding placed on each side of the outputted image (if it's within the image)
- getPaddingXY() - Method in class org.anchoranalysis.image.bean.spatial.Padding
-
Padding placed on each side of the outputted image (if it's within the image) in XY directions
- getPaddingZ() - Method in class org.anchoranalysis.image.bean.spatial.Padding
-
Padding placed on each side of the outputted image (if it's within the image) in Z direction
- getPair() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
- getPair() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
- getPair() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
-
Every combination of interactions between marks and the associated energy
- getPairAddCriteria() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- getPairAddCriteria() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
- getPairCollection() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- getPairsFor(Mark) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- getPairTypeClass() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- getParametersExperiment() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
- getParamMean() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
- getParamPrefix() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
- getParams() - Method in class org.anchoranalysis.feature.energy.EnergyStack
- getParams() - Method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
- getParams() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
-
Parameters to optionally associated with
stackEnergy, and meaningless ifstackEnergyis not specified. - getParams() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- getParams() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- getParams() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
- getParams() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- getParams() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
- getParams() - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
- getParams() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderLDAClassifier
- getParams() - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- getParams() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
- getParams() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
- getParams() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
-
Parameters used for calculating HOG
- getParams() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
-
Parameters used for calculating HOG
- getParamsOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
- getParamsOptional() - Method in interface org.anchoranalysis.feature.input.FeatureInputParams
- getParamsOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
- getParamsRequired() - Method in interface org.anchoranalysis.feature.input.FeatureInputParams
- getParamStdDev() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
- getParent() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- getParentDirectoryCreator() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
- getParentFolder() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
- getParentFolder() - Method in class org.anchoranalysis.io.manifest.file.OutputtedFile
- getParentOutputter() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
- getPartition() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.MarksFromPartition
- getPath() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
-
Path to annotation
- getPath() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
-
the path an object was not found at.
- getPath() - Method in class org.anchoranalysis.bean.shared.path.RootPath
-
A path on a filesystem to the directory, that defines the root
- getPath() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
-
The path
- getPath() - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
- getPath() - Method in class org.anchoranalysis.plugin.io.bean.filepath.StaticFilePath
- getPathAnnotation() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
- getPathDefaultMarks() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
- getPathLabel() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
-
Path to a CSV label file (comma-separated, with header, no quotes)
- getPathParams() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
- getPaths() - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
-
All files need to be present
- getPaths() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.FileSetFromStringSet
- getPayload() - Method in class org.anchoranalysis.core.graph.TypedEdge
-
The edge.
- getPayload() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
- getPenaltyValue() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
- getPeriodTriggerBank() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- getPermutation() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
-
A permutation to apply.
- getPermutations() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
-
A list of permutations to apply.
- getPermuteProperty() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
- getPermuteProperty() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
- getPermuteProperty() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
- getPixelsForPlane(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- getPlotBackgroundColor() - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- getPlotGridlineColor() - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- getPlusOne() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
- getPoints() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- getPoints() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
- getPoints() - Method in class org.anchoranalysis.spatial.Contour
- getPointsFitter() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
- getPointsFitter() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
-
Name of the
PointsFitterto use. - getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
- getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
- getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
- getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
- getPointsFitter() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- getPointsFitterSet() - Method in class org.anchoranalysis.mpp.bean.init.PointsInitParams
- getPointsFromOrientationProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
- getPointsFromOrientationXYProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- getPointsProposer() - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
- getPos() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
- getPositionProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
- getPositionProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
- getPower() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
- getPrefix() - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
-
A prefix that is placed before the name of every bean created
- getPrefix() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
- getPrefix() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
- getPrefix() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
- getPrefix() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
- getPrefixer() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
-
The
OutputManagerassociated with the experiment whichOutputteruses. - getPrependColor() - Method in class org.anchoranalysis.bean.shared.color.scheme.Prepend
- getPrependString() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
- getPrependString() - Method in class org.anchoranalysis.feature.bean.list.PrependName
- getPrependString() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
- getPrependString() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
- getPriority() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
- getProbMapID() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
- getProbMapSet() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- getProbNeg() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
- getProbPos() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
- getProperties() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- getProperty(String) - Method in class org.anchoranalysis.core.value.KeyValueParams
- getProperty(String) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- getPropertyAsDouble(String) - Method in class org.anchoranalysis.core.value.KeyValueParams
- getPropertyDefiner() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
- getPropertyInitializer() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
- getPropertyPath() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
-
Either a direct property of a bean e.g.
- getProposal() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- getProposal() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- getProposalSecondary() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
-
An optional additional marks-Energy that provides an additional explanation of proposed
- getProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
- getProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
- getProvider() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
- getPxlPartMemo() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
- getPxlPartMemo() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
- getQuantile() - Method in class org.anchoranalysis.feature.bean.results.Quantile
-
The quantile.
- getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
- getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
- getQuantile() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
- getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
- getQuantile() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
- getQuantileHigh() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
- getQuantileLow() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
- getQuantileLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
- getQuantileUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
- getRadii() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- getRadii() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- getRadiiProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
- getRadiiProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
- getRadius() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
- getRadius() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- getRadius() - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
- getRadius() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
- getRadiusBound() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
- getRadiusBound() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
- getRadiusX() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- getRadiusY() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- getRadiusZ() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- getRandomNumberGenerator() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
- getRangeAxisLimits() - Method in class org.anchoranalysis.plot.PlotInstance
- getRangeC() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
- getRangeT() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
- getRangeZ() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
- getRate() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
- getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Gets an unsigned-byte (represented as a byte) at the current buffer position.
- getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
-
Gets an unsigned-int (represented as an int) at the current buffer position.
- getRaw() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
Gets an unsigned-short (represented as a short) at the current buffer position.
- getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Gets an unsigned-byte (represented as a byte) at a particular buffer position.
- getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
-
Gets an unsigned-int (represented as a int) at a particular buffer position.
- getRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
Gets an unsigned-short (represented as a short) at a particular buffer position.
- getReason() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
- getReceive() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
- getRecordedOutputs() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules
-
If defined, records output-names that are written / not-written during the experiment.
- getRed() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
- getRed() - Method in class org.anchoranalysis.core.color.RGBColor
- getRed() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
- getReduce() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
-
Method for reducing all pairs into a single value e.g.
- getReduce() - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
-
The algorithm for reducing the number of object-masks.
- getReferencePoissonIntensity() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
- getReferencesFeatureListCreator() - Method in class org.anchoranalysis.feature.bean.list.ReferencedFeatures
-
Ensures any feature-lists mentioned here are evaluated, before this list is created.
- getReferencesFeatureListCreator() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
-
Makes sure a particular feature list creator is evaluated
- getRegex() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
- getRegex() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
-
Regular expression to match against string
- getRegex() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
A regular-expression applied to the image file-path that matches three groups.
- getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RegExMatcher
- getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.PathRegEx
-
Regular expression to use to match path with at least one group in it.
- getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
- getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
-
The regular-expression to use for matching groups.
- getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
- getRegEx() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.RemoveMatching
-
If a path matches a regular expression it is removed.
- getRegEx() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
- getRegexAdjacent() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
This needs to be set if there is at least one adjacentChannel.
- getRegExDir() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
-
If non-empty a regular-expression is applied to directories
- getRegExFile() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
-
If non-empty a regular-expression is applied to files
- getRegion() - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
- getRegion() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
- getRegionID() - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- getRegionID() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
- getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
- getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
- getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- getRegionID() - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
- getRegionID() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.FeatureMarkRegion
- getRegionID() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
- getRegionID() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
- getRegionID() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- getRegionID() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- getRegionMap() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- getRegionMap() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergyScheme
- getRegionMap() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
- getRegionMap() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
- getRegionMap() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
- getRegionMap() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
- getRegionMap() - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
- getRegionMap() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
- getRegionMap() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
- getRegionMap() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- getRegionMembership() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
- getRejectionReason() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
- getRelation() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- getRelation() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
- getRelation() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
-
Relation to threshold
- getRelation() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- getRelation() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
- getRelation() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
- getRelation() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
- getRemainder() - Method in class org.anchoranalysis.core.system.path.SplitPath
- getRepeat() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- getRepeats() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
-
Total number of births
- getReplacement() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.ApplyRegExSubstitution
- getReplacement() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
-
What to replace in the path
- getReplacement() - Method in class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile
-
The replacement string used to determine the file
- getRequireArguments() - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf
-
The conditions that must be fulfilled
- getRequireArguments() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
- getResizeTo() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
-
If set, each channel is scaled to a specific size before the mean is calculated (useful for combining different sized images)
- getResizeTo() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
-
The input-image is rescaled to this width/height before calculating HOG descriptors
- getResizeTo() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
-
The input is rescaled to this width/height before calculating HOG descriptors
- getResolution() - Method in class org.anchoranalysis.image.bean.nonbean.segment.BinarySegmentationParameters
- getResolutionOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
- getResolutionOptional() - Method in interface org.anchoranalysis.feature.input.FeatureInputWithResolution
- getResolutionOptional() - Method in class org.anchoranalysis.image.feature.histogram.FeatureInputHistogram
- getResolutionOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureInputMarkCollection
- getResolutionOptional() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
- getResolutionRequired() - Method in interface org.anchoranalysis.feature.input.FeatureInputWithResolution
- getRestrictTo() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
-
If set, the inversion only occurs on a particular region of the mask, as determined by this mask
- getResults() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
- getResultsVector() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
- getResX() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
- getResY() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
- getResZ() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
- getReverse() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
- getRGB() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
- getRGB() - Method in class org.anchoranalysis.core.color.RGBColor
- getRight() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
-
Objects on right-side of the comparison
- getRoot() - Method in class org.anchoranalysis.core.system.path.SplitPath
- getRoot() - Method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
- getRoot() - Method in class org.anchoranalysis.test.TestLoader
- getRoot1() - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
- getRoot2() - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
- getRootFolder() - Method in class org.anchoranalysis.io.manifest.Manifest
- getRootName() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
- getRootName() - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
- getRootName() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
- getRootName() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
- getRootName() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
If non-empty then a rooted filesystem is used with this root
- getRootName() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
Root-name assuming multi-rooted strucutre
- getRootName() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
- getRootNameForStructure() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
If rootInStructure==true, the rootName is placed in the folder structure.
- getRootPath() - Method in class org.anchoranalysis.plugin.io.manifest.DeserializedManifest
- getRotationAngle() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
- getRotationAngle() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
- getRotationBounds() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
- getRotationMatrix() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
- getRotationX() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
- getRotationY() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
- getRotationZ() - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
- getRotMatrix() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- getRow() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
- getRow(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
- getRowForListIndex(int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
- getRowSource() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
- getSampleEvery() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SampleWithDirectory
- getScalarProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
- getScalarProposer() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
- getScale() - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
-
Standard-Deviation
- getScale() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
-
Whether to increase or reduce the size of the images
- getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
- getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
-
Determines how much to scale by
- getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
- getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
- getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorInverted
- getScaleCalculator() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- getScaleCalculator() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
- getScaleFactor() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
- getScaleLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
-
Sets the min by multiplying the quantileLower by this constant.
- getScaleLower() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
- getScaleRadii() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
- getScaleUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
-
Sets the max by multiplying the quantileUpper by this constant.
- getScaleUpper() - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
- getScore() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- getScoreProvider() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
- getScoreThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
-
Bounding boxes with scores above this threshold are removed
- getSearchObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
- getSecond() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
- getSecond() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
- getSecond() - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
-
Output-names in the second-level (for all first level output-names)
- getSecond() - Method in class org.anchoranalysis.mpp.segment.transformer.Compose
-
Second transformation from
UtoT - getSecondary() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
- getSegment() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
- getSegment() - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
- getSegment() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
-
Segmentation algorithm
- getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
- getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
- getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
-
The segmentation procedure.
- getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
- getSegment() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
- getSegment() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
-
The segmentation algorithm
- getSegment() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
-
How to perform the segmentation.
- getSegment() - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
-
The segmentation algorithm that is applied as an input to non-maxima suppression.
- getSegmentStack() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
- getSelect() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
-
Either "merged" or "first" or "second" indicating which feature to delegate from
- getSelectChannels() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
-
Selects which channels are included, optionally renaming.
- getSemiMajorAxis() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
- getSemiMinorAxis() - Method in class org.anchoranalysis.plugin.points.bean.fitter.EllipseStandardFormConverter
- getSeperator() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
- getSeperator() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- getSequence() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequence
-
Where the sequence starts
- getSequence() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
-
First number range that is appended
- getSequence() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
- getSequenceAdditional() - Method in class org.anchoranalysis.feature.bean.list.ListSequence
-
Another number range that is appended
- getSequenceType() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed
- getSequenceType() - Method in class org.anchoranalysis.io.manifest.ManifestDirectoryDescription
-
A sequence-type to describe the different filenames outputted in the directory.
- getSeriesColors() - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
- getSeriesNameFor(int) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
- getSet() - Method in class org.anchoranalysis.feature.shared.SharedFeatureSet
- getSetPoints() - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- getSettings() - Method in class org.anchoranalysis.io.output.outputter.Outputter
- getSettings() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
-
General settings for writing outputs.
- getSharedFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
- getSharedFeatures() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
- getSharedFeatureSet() - Method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
- getSharedObjects() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
- getSharedObjects() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- getSharedState() - Method in class org.anchoranalysis.experiment.task.InputBound
- getSharedState() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
- getShellRad() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
- getShellRad() - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
- getShellRad() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- getShellRad() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- getShellRad() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
- getShellRad() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
- getShellRad() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
- getShift() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
- getShortTitle() - Method in class org.anchoranalysis.plot.bean.Plot
-
A shortened version of
Plot.getTitle(). - getShowOngoingJobsLessThan() - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
-
When the number of ongoing jobs is less than this threshold, they are shown in event logs.
- getSigma() - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
- getSigma() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
- getSimplePairCollection() - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- getSimplePairCollectionID() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- getSingle() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
- getSize() - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
- getSize() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- getSize() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
-
Size of the image produced showing a plot of the histogram
- getSize() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
-
Size of all created thumbnails
- getSize() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
- getSize() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- getSize() - Method in class org.anchoranalysis.plugin.io.multifile.IntegerRange
- getSizeHalf() - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
- getSkipFirstTrim() - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
- getSkipFirstTrim() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
- getSkipNumberSubdirectories() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
-
Initially skip this number of directories before including them in the description.
- getSlice() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
- getSlice(int) - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
- getSlice(int) - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
- getSliceEnd() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
- getSliceFirst() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
-
First slice.
- getSliceID() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
-
Index of slice to use, or -1 to use all slices
- getSliceIndex() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
-
Which slice to use from
mask - getSliceLast() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
-
Last slice.
- getSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
- getSliceStart() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
- getSmoothingFactor() - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
- getSource() - Method in class org.anchoranalysis.bean.shared.StringMapItem
- getSource() - Method in class org.anchoranalysis.image.core.object.MatchedObject
-
The source object (which is matched against others)
- getSource() - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
- getSource() - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
- getSource() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
-
Source of feature-values to be exported
- getSource() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.DualVoxelizedMarks
- getSource() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
- getSourceFolderPath() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- getSplitDescriptiveNameRegex() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- getSplitProposer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
- getSquareSize() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
- getStack() - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
- getStack() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- getStack() - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
- getStack() - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
- getStack() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
-
Provides a stack.
- getStack() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
-
The stack to segment
- getStack() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
-
The stack that is the background for our objects
- getStackEnergy() - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
-
Optionally specifies an energy-stack to be associated with every calculation input.
- getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
-
Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks)
- getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
- getStackEnergy() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
- getStackEnergy() - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
- getStackID() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
- getStackName() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
-
If defined, processing only occurs the stack with this specific stack and index.
- getStackNameVisualOriginal() - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
- getStackProviderID() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
-
Specifies the ID of an existing stack.
- getStackProviderID() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
- getStackReader() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
- getStackReader() - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- getStackReader() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
- getStackReader() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- getStackReader() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
- getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
- getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
- getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
- getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
- getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
- getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
- getStackReader() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
- getStackReader() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
The raster-reader for reading the main file
- getStackReaderAdjacent() - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
The raster-reader to use for opening any adjacent-channels
- getStackReaderAppend() - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
The raster-reader for reading any appended files
- getStackReaderHigh() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- getStackReaderInput() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- getStackReaderLow() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- getStackReaderMiddle() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- getStacksOutputEnabled() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
-
Deprecated.What's allowed or not when outputting stacks
- getStacksOutputEnabled() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- getStackStore() - Method in class org.anchoranalysis.plugin.image.task.grouped.ChannelSource
- getStart() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
-
The index to begin iteration from
- getStartIndex() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- getStartingIntensity() - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
-
The first intensity-value to consider as a valid object (e.g.
- getStartPoint() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- getState() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
- getStateReporter() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- getStrategy() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
- getStrategy() - Method in class org.anchoranalysis.feature.session.strategy.replace.bind.BoundReplaceStrategy
- getStrategy() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
- getSubdirectory() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
If non-empty than an additional subdirectory is appended as a suffix ${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
- getSubDirectory() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
- getSubdirectoryName() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
-
The name of a subdirectory in the current context to write to, or if empty, files are written into the current directory context.
- getSubtractConstant() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
- getSubtractRadii() - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
- getSuffix() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
- getSum() - Method in class org.anchoranalysis.math.arithmetic.RunningSum
-
The running sum
- getSummarizer() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
- getSummarizer() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
- getSummarizerElse() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
-
Used for summary if
count(elements) <= countThreshold - getSummarizerGreaterThan() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
-
Used for summary if
count(elements) > countThreshold - getTarget() - Method in class org.anchoranalysis.bean.shared.StringMapItem
- getTask() - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
- getTask() - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
- getTask() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
- getTask() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- getTask() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- getTask() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- getTaskName() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
-
A name to describe the ongoing task
- getTaskProcessor() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
-
What task is associated with the experiment, and how it is processed.
- getTemperature() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- getTemperature() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- getTemplateMark() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
- getTemporary() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- GetterFromIndex<T> - Interface in org.anchoranalysis.core.index
- getTermination() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
- getThreshold() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
- getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
- getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
- getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
- getThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
- getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
- getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
- getThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold
-
Only considers values greater or equal to the threshold
- getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
- getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
- getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
- getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
- getThreshold() - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
- getThreshold() - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
- getThresholder() - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
- getThresholder() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
-
The thresholder that will convert a channel into a binary-channel
- getThresholdHigh() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- getThresholdLow() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- getThumbnail() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
-
Generates a thumbnail representation of one or more objects combine, as form a single input
- getThumbnail() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
-
Method to generate a thumbnail for images
- getThumbnail() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
- getThumbnailBatch() - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
- getTime() - Method in class org.anchoranalysis.experiment.task.processor.JobState
- getTimeAnnotationLastUpdated() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
-
Number of seconds since the UNIX epoch
- getTimeIndex() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
- getTimeIndex() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- getTimeIndex() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
- getTimeIndex() - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
- getTimeIndexGroupID() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- getTimes() - Method in class org.anchoranalysis.bean.shared.color.scheme.Repeat
- getTitle() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
- getTitle() - Method in class org.anchoranalysis.plot.bean.Plot
-
The full title of the plot.
- getTitle() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
- getTo() - Method in class org.anchoranalysis.core.graph.TypedEdge
-
The vertex the edge joins to.
- getToleranceLog10() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
- getTotal() - Method in class org.anchoranalysis.feature.energy.EnergyTotal
- getTotal() - Method in class org.anchoranalysis.mpp.probmap.ProbWeights
- getTotalCount() - Method in class org.anchoranalysis.math.histogram.Histogram
- getTotalNumberTasks() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- getTransformer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartitionAndThen
- getTransformer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
- getTransformer() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
- getTransformerKernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
- getTransformerMarks() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.AddDualTransformer
- getTransformerPrimary() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
- getTransformerSecondary() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
- getTransformerStateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
- getTriggerTerminationCondition() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
- getTrimTrailingDirectory() - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
- getTrimTrailingDirectory() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
- getType() - Method in class org.anchoranalysis.io.manifest.ManifestDescription
-
Identifies the type of entity.
- getUnconvertedVoxelAt(int, Point3i) - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- getUniqueLabel() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
-
Label that uniquely identifies the ID (for machine purposes)
- getUnit() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
- getUnit() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
- getUnitConverterOptional() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
- getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
- getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
- getUnitType() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
- getUnitType() - Method in class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
- getUnitType() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
- getUnitTypeFrom() - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
- getUnitTypeTo() - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
- getUnitValueDistance() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
- getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
-
Gets an unsigned-byte (represented as a int) at the current buffer position.
- getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
- getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
-
Gets an unsigned-int (represented as a long) at the current buffer position.
- getUnsigned() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
- getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
-
Gets an unsigned-byte (represented as a int) at a particular buffer position.
- getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
- getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
-
Gets an unsigned-int (represented as a long) at a particular buffer position.
- getUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
- getUnsignedByte() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
- getUnsignedInt() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
- getUnsignedShort() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
- getUsageFooter() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
- getUsageHeader() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
- getUserFriendlyLabel() - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
-
Descriptive user-friendly label displayed via GUI
- getValue() - Method in class org.anchoranalysis.bean.NamedBean
- getValue() - Method in interface org.anchoranalysis.core.identifier.name.NameValue
-
The associated value
- getValue() - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
- getValue() - Method in class org.anchoranalysis.core.value.TypedValue
- getValue() - Method in class org.anchoranalysis.feature.bean.operator.Constant
- getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
- getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
- getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
- getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
- getValue() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
- getValue() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
-
The value.
- getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
- getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
- getValue() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
- getValue() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
- getValue() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
- getValue() - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
- getValue() - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorConstant
- getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
- getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- getValue() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
- getValue() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
- getValue() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
- getValue() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Constant
- getValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
- getValueIfEmpty() - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
-
The value to return iff
exceptionifEmptyis false - getValueIfTooFewVoxels() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
-
A value to return if there are too few voxels (less than
MIN_NUM_VOXELSto calculate moments - getValueNoObject() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
- getValueNoObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
- getValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
- getValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
-
The values of the string-set
- getVersion() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
- getVersionFooter() - Method in class org.anchoranalysis.launcher.config.ResourcesConfig
- getVertex() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
- getVerticalAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
- getVisitScheduler() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
- getVoxelDataType() - Method in class org.anchoranalysis.image.core.channel.Channel
- getVoxelDataType() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- getVoxels() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
- getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
- getVoxelsConverter() - Method in interface org.anchoranalysis.image.core.channel.convert.attached.ChannelConverterAttached
- getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
- getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
- getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
- getVoxelsConverter() - Method in class org.anchoranalysis.image.core.channel.convert.ChannelConverter
- getWeight() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
- getWeight() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
- getWeightBackground() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
- getWeightedKernelFactory(int) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- getWeightForeground() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
- getWeightItem1Greater() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
- getWeightItem2Greater() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
- getWeightNegative() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposerOption
- getWeightNegative() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
- getWeightNegative() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
- getWeightPositive() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposerOption
- getWeightPositive() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
- getWeightPositive() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
- getWeightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
- getWhenDetailed() - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
-
Logger to use when detailed-logging is on
- getWhenEqual() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
- getWhenNot() - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
-
Logger to use when detailed-logging is off
- getWhenNotEqual() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
- getWhenOneOrThreeChannels() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
-
Writer employed if a stack is a one or three-channeled image, that is not 3D, and not RGB.
- getWhenRGB() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
-
Writer employed if a stack is a three-channeled RGB image and is not 3D.
- getWidth() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
- getWidth() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
-
Width (what the difference is divided by)
- getWidthFactor() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
- getWindowSize() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
- getWindowSize() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
-
The window-size as per OpenCV implementation.
- getWithin() - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
-
Returned as a constant if a value lies within the range
- getWithinValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
-
Constant to return if value lies within the range
- getWithinValue() - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
-
Constant to return if value lies within the range
- getWriter() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput
- getWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
-
Default writer, if a more specific writer is not specified for a condition.
- getWriter() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
- getWriterAlways2D() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
-
Writer to use if it is guaranteed that the image will always be 2D.
- getWriterElse() - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
-
Otherwise the writer to use.
- getWriterInstance(Class<?>) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
-
Gets a writer-instance for a particular
writerParentClass. - getWriters() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
-
Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)
- getWriters() - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
-
The writers associated with this output-manager.
- getX() - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
- getX() - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
- getXMax(Point3i, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
- getXMin(Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
- getXmlAggregatedGroup() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
-
The name of the XML file outputted with aggregated values for each group, if enabled.
- getXMLConfiguration() - Method in class org.anchoranalysis.experiment.bean.Experiment
- getY() - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
- getY() - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
- getYAxisLowerMargin() - Method in class org.anchoranalysis.plot.index.LinePlot
- getYAxisUpperMargin() - Method in class org.anchoranalysis.plot.index.LinePlot
- getYMax(Point3i, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
- getYMin(Point3i) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
- getYVal(T, int) - Method in interface org.anchoranalysis.plot.index.LinePlot.YValGetter
- getYValGetter() - Method in class org.anchoranalysis.plot.index.BarPlot
- getYValGetter() - Method in class org.anchoranalysis.plot.index.LinePlot
- getZ() - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
- getZAlign() - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
- getZSliceGroupID() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- getZSliceNum() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
- getZSliceNum() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- getZSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
- GlobalRegionIdentifiers - Class in org.anchoranalysis.mpp.mark
- GradientBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
- GradientBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
- GradientBaseAddSum - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
- GradientBaseAddSum() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
- gradientCalculation() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
- GradientForAxis - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Extracts the gradient in the direction of a particular axis (identified by an index)
- GradientForAxis() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
- GradientMagnitude - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
- GradientMagnitude() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMagnitude
- GradientMeanForAxis - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
-
Calculates the mean of the intensity-gradient defined by multiple Energy channels in a particular direction
- GradientMeanForAxis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
- GradientXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
Gradient in x and y axes
- GradientXY() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientXY
- GraphLogger - Class in org.anchoranalysis.plugin.image.object.merge
- GraphLogger(DescribeGraph, Logger) - Constructor for class org.anchoranalysis.plugin.image.object.merge.GraphLogger
- GraphWithoutPayload<V> - Class in org.anchoranalysis.core.graph
-
A graph, either directed or undirected, where edges contain no payload.
- GraphWithoutPayload(boolean) - Constructor for class org.anchoranalysis.core.graph.GraphWithoutPayload
-
Creates the graph.
- GraphWithPayload<V,P> - Class in org.anchoranalysis.core.graph
-
A graph, either directed or undirected, with edges containing a payload of type
E. - GraphWithPayload(boolean) - Constructor for class org.anchoranalysis.core.graph.GraphWithPayload
-
Creates the graph.
- GrayscaleReconstruction2DIJ - Class in org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
- GrayscaleReconstruction2DIJ() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction.GrayscaleReconstruction2DIJ
- GrayscaleReconstructionByErosion - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
- GrayscaleReconstructionByErosion() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionByErosion
- GrayscaleReconstructionRobinson - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
- GrayscaleReconstructionRobinson() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionRobinson
- greaterEqualThan(VarianceCalculator) - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
- GreaterIntersectionWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Only accepts an object if it has greater (or EQUAL) intersection with
objectsGreaterthanobjectsLesser - GreaterIntersectionWith() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
- GreaterThan - Class in org.anchoranalysis.math.relation
- GreaterThan() - Constructor for class org.anchoranalysis.math.relation.GreaterThan
- GreaterThanBean - Class in org.anchoranalysis.bean.shared.relation
- GreaterThanBean() - Constructor for class org.anchoranalysis.bean.shared.relation.GreaterThanBean
- GreaterThanEqualTo - Class in org.anchoranalysis.math.relation
- GreaterThanEqualTo() - Constructor for class org.anchoranalysis.math.relation.GreaterThanEqualTo
- GreaterThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation
- GreaterThanEqualToBean() - Constructor for class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
- GreaterThanThreshold - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
-
Thresholds a histogram using a CalculateLevel keeping only the values greater equal than the threshold
- GreaterThanThreshold() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
- GreatestAreaSlice - Class in org.anchoranalysis.plugin.mpp.bean.region
- GreatestAreaSlice() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
- greedyMatch() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
-
Find a valid matching by greedily selecting among zero-cost matchings.
- green() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- GroupedAnnotationLabels - Class in org.anchoranalysis.plugin.annotation.bean.label
-
A set of annotation labels partitoned into their unique groups
- GroupedAnnotationLabels(Collection<AnnotationLabel>) - Constructor for class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels
- groupedLabels() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
- GroupedMeanChannelTask - Class in org.anchoranalysis.plugin.image.task.bean.grouped.raster
-
Creates a an aggregated-image for each group, where each voxel-value is the mean voxel-value across the group.
- GroupedMeanChannelTask() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
- GroupedSharedState<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped
-
Commonality between shared state for gouped export tasks
- GroupedSharedState(Function<ConsistentChannelChecker, GroupMapByName<S, T>>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.GroupedSharedState
- GroupedStackBase<S,T> - Class in org.anchoranalysis.plugin.image.task.bean.grouped
-
Base class for stacks (usually each channel from an image) that are somehow grouped-together.
- GroupedStackBase() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
- GroupFiles - Class in org.anchoranalysis.plugin.io.bean.groupfiles
-
An input-manager that can group together files to form stacks or time-series based on finding patterns in the file path (via regular expressions)
- GroupFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner
- groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
- groupForKey(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
- GroupingRoot - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a set of definitions of classes can be collectively grouped using this class.
- GroupMapByName<S,T> - Class in org.anchoranalysis.plugin.image.task.grouped
-
Adds items to aggregate structures identified uniquely by a name, and allows these items to be later outputted.
- GroupMapByName(String, String, Supplier<T>) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName
-
Creates a group-map.
- groupNameSet() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.IndexedCSVRows
- GroupWriter - Class in org.anchoranalysis.feature.io.results.group
-
Writes outputs pertaining to groups to the filesystem.
- GroupWriter(ResultsWriterMetadata) - Constructor for class org.anchoranalysis.feature.io.results.group.GroupWriter
- growBuffer(Point3i, Point3i, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- growBuffer(Point3i, Point3i, Optional<Extent>, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
Grows buffer of the object-mask in positive and negative directions by a certain amount.
- growBy(int) - Method in class org.anchoranalysis.spatial.Extent
- growBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
- growBy(Tuple3i, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
- growToZ(int) - Method in interface org.anchoranalysis.image.core.object.seed.Seed
- growToZ(int) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- growToZ(int) - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
- growToZ(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- growToZ(int, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
- guaranteedImageAttributes() - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
- guaranteedImageAttributes() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksAsUniqueValueGenerator
- guaranteedImageAttributes() - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
- GuessDimensions - Class in org.anchoranalysis.plugin.image.bean.dimensions.provider
-
Guesses dimensions from the input-image if it exists.
- GuessDimensions() - Constructor for class org.anchoranalysis.plugin.image.bean.dimensions.provider.GuessDimensions
H
- has(int) - Method in interface org.anchoranalysis.core.color.ColorIndex
- has(int) - Method in class org.anchoranalysis.core.color.ColorIndexModulo
- has(int) - Method in class org.anchoranalysis.core.color.ColorList
- has(int) - Method in class org.anchoranalysis.core.color.SingleColor
- has(K) - Method in class org.anchoranalysis.core.cache.LRUCache
- has(T) - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
-
Checks whether the cache contains a particular input already.
- hasAboveZero() - Method in class org.anchoranalysis.math.histogram.Histogram
- hasAllRequiredArguments(boolean) - Method in class org.anchoranalysis.experiment.bean.require.RequireArguments
- hasAllRequiredArguments(boolean) - Method in class org.anchoranalysis.experiment.bean.require.RequireDebugMode
- hasArray() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
-
Whether the buffer has an array?
- hasAtLeastOneDisabled() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
-
If there is at least one disabled output.
- hasAtLeastOneDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
-
If there is at least one disabled output.
- hasAtLeastOneEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
-
If there is at least one enabled output.
- hasAtLeastOneMultiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
-
Multiplex between
RecordedOutputs.hasAtLeastOneEnabled()andRecordedOutputs.hasAtLeastOneDisabled(). - hasBeenInit() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
- hasBeenInitialized() - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
- hasCachedCalculation() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
- hasChannel(String) - Method in class org.anchoranalysis.plugin.image.task.channel.ChannelGetterForTimepoint
- hasColorGetter() - Method in class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
- hasEqualXAndY() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- HasFriendlyErrorMessage - Interface in org.anchoranalysis.core.exception.friendly
-
Methods for extracting a user-friendly error description
- hashCode() - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
- hashCode() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
- hashCode() - Method in class org.anchoranalysis.annotation.io.image.findable.Found
- hashCode() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
- hashCode() - Method in interface org.anchoranalysis.bean.GenerateUniqueParameterization
- hashCode() - Method in class org.anchoranalysis.bean.shared.path.RootPath
- hashCode() - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
- hashCode() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
- hashCode() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
- hashCode() - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
- hashCode() - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
- hashCode() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
- hashCode() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- hashCode() - Method in class org.anchoranalysis.core.color.RGBColor
- hashCode() - Method in class org.anchoranalysis.core.concurrency.WithPriority
- hashCode() - Method in class org.anchoranalysis.core.graph.TypedEdge
- hashCode() - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
- hashCode() - Method in class org.anchoranalysis.core.index.Indexable
- hashCode() - Method in class org.anchoranalysis.core.log.CommonContext
- hashCode() - Method in class org.anchoranalysis.core.system.path.SplitPath
- hashCode() - Method in class org.anchoranalysis.core.value.TypedValue
- hashCode() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
- hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
- hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculation
- hashCode() - Method in class org.anchoranalysis.feature.calculate.cache.ResolvedCalculationMap
- hashCode() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
- hashCode() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
- hashCode() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
- hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
- hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputNull
- hashCode() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
- hashCode() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
- hashCode() - Method in class org.anchoranalysis.feature.io.name.CombinedName
- hashCode() - Method in class org.anchoranalysis.feature.io.name.SimpleName
- hashCode() - Method in class org.anchoranalysis.feature.results.ResultsVector
- hashCode() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
- hashCode() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
- hashCode() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevel
- hashCode() - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
- hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
- hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
- hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
- hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
- hashCode() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
- hashCode() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- hashCode() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- hashCode() - Method in class org.anchoranalysis.image.core.mask.Mask
- hashCode() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
- hashCode() - Method in class org.anchoranalysis.image.core.object.MatchedObject
- hashCode() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- hashCode() - Method in class org.anchoranalysis.image.core.orientation.Orientation
- hashCode() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- hashCode() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
- hashCode() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
- hashCode() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
- hashCode() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
- hashCode() - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
- hashCode() - Method in class org.anchoranalysis.image.core.stack.Stack
- hashCode() - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
- hashCode() - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair
- hashCode() - Method in class org.anchoranalysis.image.feature.object.calculation.CalculateNumVoxels
- hashCode() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputObjectCollection
- hashCode() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
- hashCode() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
- hashCode() - Method in class org.anchoranalysis.image.feature.stack.FeatureInputStack
- hashCode() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValues
- hashCode() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
- hashCode() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
- hashCode() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
- hashCode() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
- hashCode() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- hashCode() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
- hashCode() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
- hashCode() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
- hashCode() - Method in class org.anchoranalysis.io.manifest.file.FileType
- hashCode() - Method in class org.anchoranalysis.io.manifest.ManifestDescription
- hashCode() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
- hashCode() - Method in class org.anchoranalysis.io.output.outputter.Outputter
- hashCode() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
- hashCode() - Method in class org.anchoranalysis.launcher.config.HelpConfig
- hashCode() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
- hashCode() - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
- hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
- hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- hashCode() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
- hashCode() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.CalculateDeriveSingleMemoFromPair
- hashCode() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureInputMark
- hashCode() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
- hashCode() - Method in class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
- hashCode() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
- hashCode() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
- hashCode() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
- hashCode() - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
- hashCode() - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
- hashCode() - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
- hashCode() - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
- hashCode() - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
- hashCode() - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
- hashCode() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
- hashCode() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
- hashCode() - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
- hashCode() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- hashCode() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
- hashCode() - Method in class org.anchoranalysis.overlay.IndexableOverlays
- hashCode() - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
- hashCode() - Method in class org.anchoranalysis.overlay.Overlay
- hashCode() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
- hashCode() - Method in class org.anchoranalysis.plot.AxisLimits
- hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
- hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupObject
- hashCode() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
- hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
- hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
- hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
- hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
- hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
- hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
- hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
- hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
- hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
- hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
- hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
- hashCode() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.CalculateIntersecting
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.CalculateDeriveObjectInput
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegate
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.delegate.CalculateInputFromDelegateOption
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateIncrementalOperationMap
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilationMap
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosionMap
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogram
- hashCode() - Method in class org.anchoranalysis.plugin.image.feature.stack.calculation.CalculateHistogramMasked
- hashCode() - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
- hashCode() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
- hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
- hashCode() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
- hashCode() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
- hashCode() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
- hashCode() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
- hashCode() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
- hashCode() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskEverythingNonZero
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.AllSlicesMaskNonZero
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSlice
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceBase
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.bean.region.Specific
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkCollectionInput
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CalculateDeriveMarkInput
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlap
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMask
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIP
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPBase
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.feature.overlap.CalculateOverlapMIPRatio
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
- hashCode() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
- hashCode() - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
- hashCode() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.CalculatePointsFromOutline
- hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.CalculateEllipseLeastSquares
- hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
- hashCode() - Method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
- hashCode() - Method in class org.anchoranalysis.spatial.box.BoundingBox
- hashCode() - Method in class org.anchoranalysis.spatial.Extent
- hashCode() - Method in class org.anchoranalysis.spatial.point.Point2d
- hashCode() - Method in class org.anchoranalysis.spatial.point.Point2f
- hashCode() - Method in class org.anchoranalysis.spatial.point.Point2i
- hashCode() - Method in class org.anchoranalysis.spatial.point.Point3d
- hashCode() - Method in class org.anchoranalysis.spatial.point.Point3f
- hashCode() - Method in class org.anchoranalysis.spatial.point.Point3i
- hashCode() - Method in class org.anchoranalysis.spatial.point.Tuple3d
- hashCode() - Method in class org.anchoranalysis.spatial.point.Tuple3f
- hashCode() - Method in class org.anchoranalysis.spatial.point.Tuple3i
- hashCode() - Method in class org.anchoranalysis.spatial.point.Vector3d
- hashCode() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
- hasIdenticalXY() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
- hasInputFilterExtensions() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
- hasIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- hasIntersectingVoxels(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Determines whether there are any intersecting voxels on two object-masks.
- hasIntersectingVoxels(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.CountVoxelsIntersectingObjects
-
Determines whether there are any intersecting voxels on two object-masks.
- hasKey(U) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
- hasLastDivider() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- hasMatch(String) - Method in class org.anchoranalysis.bean.shared.regex.RegEx
-
Returns a boolean whether the regular-expression successfully matches a string or not
- hasMoreThanOneSlice() - Method in class org.anchoranalysis.image.core.stack.Stack
-
Does the stack have more than one slice in the z-dimension?
- hasNecessaryExtents() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
- hasNext() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble.DoubleRange
- hasNext() - Method in interface org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement.TableCreator
- hasNext() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
- hasNoCombinableNestedExceptions() - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
-
Are there nested-exceptions (according to our traversal rules) that are combinable?
- hasNoNulls() - Method in class org.anchoranalysis.feature.results.ResultsVector
- hasOffVoxel() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- hasOneSlice() - Method in class org.anchoranalysis.feature.energy.EnergyStack
-
Does exactly one z-slice exist in the energy stack?
- hasOnVoxel() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- hasOption(String) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter
-
Identical to
CommandLine.hasOption(java.lang.String). - hasPoint(Point3f) - Method in class org.anchoranalysis.spatial.Contour
- hasProperty(String) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- hasRemaining() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
-
Whether there are elements between the current position and the limit
Buffer.hasRemaining(). - hasRemaining() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
-
Are there voxels remaining in a buffer?
- hasSingleFeature() - Method in class org.anchoranalysis.feature.session.SequentialSession
- hasTemporary() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- HasTouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
-
A simple scheme for counting the touching voxels.
- HasTouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.HasTouchingVoxels
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
-
Is the execution-time of the task per-input expected to be very quick to execute?
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.experiment.bean.task.HelloWorld
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.experiment.bean.task.Task
-
Is the execution-time of the task per-input expected to be very quick to execute?
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
- hasVeryQuickPerInputExecution() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
- hasWrittenHeaders() - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
- head() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
- headers() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
- headers() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
- headers() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- HelloWorld<S extends InputFromManager> - Class in org.anchoranalysis.experiment.bean.task
-
A dummy task that simply writes a message to all log files, specifically: 1.
- HelloWorld() - Constructor for class org.anchoranalysis.experiment.bean.task.HelloWorld
- help() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
-
Config for displaying help message
- HelpConfig - Class in org.anchoranalysis.launcher.config
- HelpConfig(String, String) - Constructor for class org.anchoranalysis.launcher.config.HelpConfig
- HelperFriendlyExceptions - Class in org.anchoranalysis.bean.xml.error
-
Converts certain exceptions that occur from XML-Parsing into a friendly form to display to the user
- HelperListUtilities - Class in org.anchoranalysis.bean.xml.factory
-
Utilities for manipulating list of beans
- hexString() - Method in class org.anchoranalysis.core.color.RGBColor
- higherCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
- higherCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
- higherCountExistsThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate
-
Whether the count is greater than a particular threshold.
- highestConfidence() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
- histogram() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
- histogram() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
- histogram() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
- histogram() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- histogram(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
- Histogram - Class in org.anchoranalysis.math.histogram
- Histogram(int) - Constructor for class org.anchoranalysis.math.histogram.Histogram
- Histogram(int, int) - Constructor for class org.anchoranalysis.math.histogram.Histogram
- Histogram.BinConsumer - Interface in org.anchoranalysis.math.histogram
-
Consumers a bin and corresponding count.
- HistogramFactory - Class in org.anchoranalysis.image.voxel.statistics
- HistogramFixture - Class in org.anchoranalysis.test.feature.plugins
- HistogramFromObjectsFactory - Class in org.anchoranalysis.image.core.object
- HistogramProvider - Class in org.anchoranalysis.image.bean.provider
- HistogramProvider() - Constructor for class org.anchoranalysis.image.bean.provider.HistogramProvider
- HistogramProviderUnary - Class in org.anchoranalysis.image.bean.provider
- HistogramProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
- histograms() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- HISTOGRAMS - Static variable in class org.anchoranalysis.mpp.segment.define.OutputterDirectories
-
Where collections of histograms are typically placed in a define-experiment output
- HistogramStatistics - Class in org.anchoranalysis.math.histogram
-
Further statistics that can be derived from a histogram in addition to those callable directly from the
Histogramclass - HistogramThresholder - Class in org.anchoranalysis.plugin.image.intensity
- HOGDescriptor - Class in org.anchoranalysis.plugin.opencv.bean.feature
-
Creates the entire HOG descriptor for an image.
- HOGDescriptor() - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
- HOGFeature - Class in org.anchoranalysis.plugin.opencv.bean.feature
-
One part of a Histogram of Oriented Gradients descriptor, as applied to an image stack.
- HOGFeature() - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
- HOGFeature(SizeXY, int) - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
- HOGParameters - Class in org.anchoranalysis.plugin.opencv.bean.feature
-
Parameters for calculating a HOG Descriptor covering window-size, block-size etc.
- HOGParameters() - Constructor for class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
- HomeSubdirectory - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
- HomeSubdirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
- HorizontalCalculationCache<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.cache.horizontal
-
Caches CachedCalculations that occur repeatedly across many features, and store similar child caches.
- HorizontalCalculationCacheFactory - Class in org.anchoranalysis.feature.session.cache.horizontal
- HorizontalCalculationCacheFactory() - Constructor for class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCacheFactory
- HorizontalFeatureCache<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.cache.horizontal
-
Caches repeated-calls to the same feature, or references to a feature by an ID-value
- HorizontalFeatureCacheFactory - Class in org.anchoranalysis.feature.session.cache.horizontal
- HorizontalFeatureCacheFactory() - Constructor for class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCacheFactory
- HSB - Class in org.anchoranalysis.bean.shared.color.scheme
- HSB() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.HSB
- HungarianAlgorithm - Class in org.anchoranalysis.math.optimization
-
An implementation of the Hungarian algorithm for solving the assignment problem.
- HungarianAlgorithm(double[][]) - Constructor for class org.anchoranalysis.math.optimization.HungarianAlgorithm
-
Construct an instance of the algorithm.
I
- idAndIncrement() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
- Identifiable - Interface in org.anchoranalysis.overlay.identifier
- IdentifiablePair<T extends Identifiable> - Class in org.anchoranalysis.mpp.pair
-
Pair of marks
- IdentifiablePair(T, T) - Constructor for class org.anchoranalysis.mpp.pair.IdentifiablePair
- identifier() - Method in class org.anchoranalysis.mpp.mark.Mark
- identifier() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- identifier(Optional<String>) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifier
-
Creates an identifier for the experiment
- identifier(Optional<String>) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
- identifier(Optional<String>) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
- IdentifierByProperty - Class in org.anchoranalysis.image.core.object.properties
- IdentifierByProperty(String) - Constructor for class org.anchoranalysis.image.core.object.properties.IdentifierByProperty
- IdentifierFromMark - Class in org.anchoranalysis.mpp.mark
- IdentifierFromMark() - Constructor for class org.anchoranalysis.mpp.mark.IdentifierFromMark
- IdentifierFromOverlay - Class in org.anchoranalysis.overlay.identifier
- IdentifierFromOverlay() - Constructor for class org.anchoranalysis.overlay.identifier.IdentifierFromOverlay
- IdentifierGetter<T> - Interface in org.anchoranalysis.core.identifier.getter
- IdentifierModulo<T> - Class in org.anchoranalysis.core.identifier.getter
- IdentifierModulo() - Constructor for class org.anchoranalysis.core.identifier.getter.IdentifierModulo
- IdentifierModulo(IdentifierGetter<T>, int) - Constructor for class org.anchoranalysis.core.identifier.getter.IdentifierModulo
- IdentifyByIteration<T> - Class in org.anchoranalysis.core.identifier.getter
- IdentifyByIteration() - Constructor for class org.anchoranalysis.core.identifier.getter.IdentifyByIteration
- IdentifyDelegateToOverlays - Class in org.anchoranalysis.overlay.identifier
- IdentifyDelegateToOverlays(IdentifierGetter<Overlay>, ColoredOverlayCollection) - Constructor for class org.anchoranalysis.overlay.identifier.IdentifyDelegateToOverlays
- IdentifyDelegateToOverlays(IdentifierGetter<Overlay>, ColoredOverlayCollection, boolean) - Constructor for class org.anchoranalysis.overlay.identifier.IdentifyDelegateToOverlays
- IdentifyObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
-
Assigns a unique id number to each object.
- IdentifyObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.IdentifyObjects
- Identity - Class in org.anchoranalysis.plugin.image.feature.bean.score
- Identity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.Identity
- IdentityImposeValueRelationToHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.score
- IdentityImposeValueRelationToHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- idFor(ObjectWithProperties, int) - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
-
ID for a particular object
- IfCondition<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.conditional
-
The result of featureCondition is compared to a threshold, and then either the underlying feature is calculated (positive case), or featureElse is (negative case)
- IfCondition() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
- IfConditionWithinRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
Calculates a value if a condition lies within a certain range, otherwise returns constants
- IfConditionWithinRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
- IfGreaterThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Calculates a level from the first delegate and if greater than a threshold, recalculates from a second delegate.
- IfGreaterThan() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
- IfHighLow - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation
iff first==HIGH and second==LOW then LOWvoxelwise on both masks, modifying {mask} with the result. - IfHighLow() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.IfHighLow
- IfKeyValueCondition - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current
maskis returned if a condition on key-values is satisfied otherwisemaskElseis returned. - IfKeyValueCondition() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
- IfLessThan - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Calculates a level from the first delegate and if less than a threshold, recalculates from a second delegate.
- IfLessThan() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
- IfNotEmpty - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current
maskis returned if it's non-empty (at least one ON voxel) otherwisemaskElseis returned. - IfNotEmpty() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfNotEmpty
- IfObjectFilter - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current
maskis returned if the mask (treated as an object) passed an object-filter, otherwisemaskElseis returned. - IfObjectFilter() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
- IfOutsideRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
Clips a value if it lies outside the range - instead returning particular constants if below or above an acceptable range
- IfOutsideRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.IfOutsideRange
- IfParamEqual - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Multiplexes between two object-collection-providers depending on whether a parameter value equals a particular string
- IfParamEqual() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
- IfParamEquals - Class in org.anchoranalysis.plugin.image.bean.channel.provider
- IfParamEquals() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
- IfPredicateBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
Base class which multiplexes between the current mask and an alternative depending if a condition is met.
- IfPredicateBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
- ifPresent(Optional<S>, CheckedConsumer<S, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
-
Like
Optional.map(java.util.function.Function<? super T, ? extends U>)but tolerates an exception in the mapping function, which is immediately thrown. - ifPresentSingle(String, CheckedConsumer<String, E>) - Method in class org.anchoranalysis.launcher.options.CommandLineExtracter
-
Executes a
Consumerif an option is present. - IfStackExists - Class in org.anchoranalysis.plugin.image.bean.mask.provider.predicate
-
The current
maskis a particular stack exists (at least one ON voxel) otherwisemaskElseis returned. - IfStackExists() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
- IfVoxelZero - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Creates a new channel which is a merged version of two input channels according to rules.
- IfVoxelZero() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
- ignoreAtThreshold - Variable in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3Base
-
Disconsiders anything outside the threshold.
- IgnoreUnderscorePrefix - Class in org.anchoranalysis.io.output.bean.enabled
-
All outputs are allowed unless the name's first character is an underscore.
- ImageAssignLabel<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
Assigns a label to each image and optionally 1.
- ImageAssignLabel() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
- ImageBean<T> - Class in org.anchoranalysis.image.bean
- ImageBean() - Constructor for class org.anchoranalysis.image.bean.ImageBean
- ImageCSVLabeller - Class in org.anchoranalysis.plugin.image.task.bean.labeller
- ImageCSVLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
- ImageCSVLabellerInitParams - Class in org.anchoranalysis.plugin.image.task.labeller
- ImageCSVLabellerInitParams(FileLabelMap<String>) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
- ImageFileShape - Class in org.anchoranalysis.io.bioformats.copyconvert
-
How to shape the image (across various dimensions) after the copying
- ImageFileShape(Dimensions, int, int) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
- ImageInitParams - Class in org.anchoranalysis.image.bean.nonbean.init
- ImageInitParams(SharedObjects) - Constructor for class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- ImageIOWriter - Class in org.anchoranalysis.plugin.io.bean.stack.writer
- ImageIOWriter() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.ImageIOWriter
- ImageJRasterWriter - Class in org.anchoranalysis.io.imagej.bean.stack.writer
-
Base class for writing a raster using ImageJ.
- ImageJRasterWriter() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter
- ImageLabelAnnotation - Class in org.anchoranalysis.annotation.image
-
A single label that pertains to an image.
- ImageLabelAnnotation(String) - Constructor for class org.anchoranalysis.annotation.image.ImageLabelAnnotation
- ImageLabeller<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
Associates a label with an image.
- ImageLabeller() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller
- ImageLabellerStringMap<T> - Class in org.anchoranalysis.plugin.image.task.bean.labeller
-
Maps one set of labels to another
- ImageLabellerStringMap() - Constructor for class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
- ImageLabellerStringMapInitParams<T> - Class in org.anchoranalysis.plugin.image.task.labeller
- ImageLabellerStringMapInitParams(Map<String, String>, T) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
- ImageMoments - Class in org.anchoranalysis.math.moment
-
The first moment (mean) and eigenvalues of the second moments (covariance) from a matrix of points
- ImageMoments(DoubleMatrix2D, boolean, boolean) - Constructor for class org.anchoranalysis.math.moment.ImageMoments
-
Calculates the second-moments from the covariance of a matrix of points
- ImageMomentsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
A base class for features that are calculated using image-moments
- ImageMomentsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
- ImageSize - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
-
Summarizes the size of images.
- ImageSize() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.ImageSize
- ImgLib2Lanczos - Class in org.anchoranalysis.image.bean.interpolator
- ImgLib2Lanczos() - Constructor for class org.anchoranalysis.image.bean.interpolator.ImgLib2Lanczos
- ImgLib2Linear - Class in org.anchoranalysis.image.bean.interpolator
- ImgLib2Linear() - Constructor for class org.anchoranalysis.image.bean.interpolator.ImgLib2Linear
- immutableAdd(Point2i, Point2i) - Static method in class org.anchoranalysis.spatial.point.Point2i
-
Performs an addition without changing any values in an existing point
- immutableAdd(Point3d, int, int, int) - Static method in class org.anchoranalysis.spatial.point.Point3d
-
Performs an addition without changing any values in an existing point
- immutableAdd(ReadableTuple3i, int, int, int) - Static method in class org.anchoranalysis.spatial.point.Point3i
-
Performs an addition without changing any values in an existing point
- immutableAdd(ReadableTuple3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.Point3i
-
Performs an addition without changing any values in an existing point
- immutableAdd(Tuple3d, Tuple3d) - Static method in class org.anchoranalysis.spatial.point.Point3d
-
Performs an addition without changing any values in an existing point
- immutableScale(ReadableTuple3i, int) - Static method in class org.anchoranalysis.spatial.point.Point3i
-
Performs a scale without changing any values in an existing point
- immutableScale(Tuple3d, int) - Static method in class org.anchoranalysis.spatial.point.Point3d
-
Performs a scale without changing any values in an existing point
- immutableSubtract(ReadableTuple3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.point.Point3i
-
Performs a subtraction without changing any values in an existing point
- immutableSubtract(Tuple3d, Tuple3d) - Static method in class org.anchoranalysis.spatial.point.Point3d
-
Performs a subtraction without changing any values in an existing point
- imposeMinima(Channel, SeedCollection, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImposition
- imposeMinima(Channel, SeedCollection, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
- ImposeMinima - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Imposes minima in seed locations on the input-channel before performing the segmentation
- ImposeMinima() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
- imposeMinimumRadius(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- ImposeResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader
- ImposeResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
- IncludeBeanFactory - Class in org.anchoranalysis.bean.xml.factory
- IncludeBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.IncludeBeanFactory
- includeFirst() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
- includeFirstOrSecond() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
- includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
-
Iff true, group columns are added to the CSV exports, and other group exports may occur in sub-directories.
- includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
- includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
- includeGroupInExperiment(boolean) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
-
If either a group-generator is defined or there's more than one provider, then groups should be included
- IncludeListFactory<T> - Class in org.anchoranalysis.bean.xml.factory
- IncludeListFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.IncludeListFactory
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaPair
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
- includeMarks(VoxelizedMarkMemo, VoxelizedMarkMemo, Dimensions, Optional<FeatureCalculatorMulti<FeatureInputPairMemo>>, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
- IncludeMarksFailureException - Exception in org.anchoranalysis.mpp.feature.addcriteria
- IncludeMarksFailureException(Exception) - Constructor for exception org.anchoranalysis.mpp.feature.addcriteria.IncludeMarksFailureException
- IncludeMarksFailureException(String) - Constructor for exception org.anchoranalysis.mpp.feature.addcriteria.IncludeMarksFailureException
- includeMerged() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
- includePossiblyOverlappingObject(ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
- includePossiblyOverlappingObject(T, T) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
- includePossiblyOverlappingObject(T, T) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
-
Whether to include another (possibly-overlapping with
source) element in processing? - IncludeRandomObjects - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points
-
1.
- IncludeRandomObjects() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
- includeSecond() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
- IncompleteElementRange - Interface in org.anchoranalysis.io.manifest.sequencetype
-
An incomplete range of discrete integers (like
BoundedRangeIncompletebut with a string-representation for each index. - IncorrectImageSizeException - Exception in org.anchoranalysis.image.core.dimensions
- IncorrectImageSizeException(Exception) - Constructor for exception org.anchoranalysis.image.core.dimensions.IncorrectImageSizeException
- IncorrectImageSizeException(String) - Constructor for exception org.anchoranalysis.image.core.dimensions.IncorrectImageSizeException
- IncorrectVoxelTypeException - Exception in org.anchoranalysis.image.voxel.datatype
- IncorrectVoxelTypeException(String) - Constructor for exception org.anchoranalysis.image.voxel.datatype.IncorrectVoxelTypeException
- IncorrectVoxelTypeException(Throwable) - Constructor for exception org.anchoranalysis.image.voxel.datatype.IncorrectVoxelTypeException
- incr(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
- incr(Reporting<S>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodTriggerBank
- incrCount(T) - Method in class org.anchoranalysis.plugin.io.summarizer.FrequencyMap
- IncreaseFeatureCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
- IncreaseFeatureCondition(FeatureEvaluator<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
- increasingIntegers(OutputPatternIntegerSuffix) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
- IncreasingIntegers - Class in org.anchoranalysis.io.manifest.sequencetype
-
Indices must be integers that always increase as added.
- IncreasingIntegers() - Constructor for class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
- increment() - Method in class org.anchoranalysis.math.arithmetic.Counter
- increment(double) - Method in class org.anchoranalysis.math.arithmetic.RunningSum
-
Adds a new item to the sum, and increments the count by 1.
- increment(double, long) - Method in class org.anchoranalysis.math.arithmetic.RunningSum
-
Increments both the sum and count by particular values
- increment(RunningSum) - Method in class org.anchoranalysis.math.arithmetic.RunningSum
-
Increments (adds) an existing
RunningSumto the current. - increment(Point2d) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
- increment(Point2i) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
- increment(Point3d) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
- increment(Point3i) - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
- increment(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- incrementCount(T) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannels
- incrementingByOne(OutputPatternIntegerSuffix) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
-
Writes elements to
directory, with an incrementing integer in the filename. - incrementingByOneCurrentDirectory(String, String, int) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
-
Writes elements to the current directory, with an incrementing integer in the filename.
- incrementingByOneStream(OutputPatternIntegerSuffix, Stream<T>) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
-
Writes file for each element in a stream with an incrementing integer sequence in the outputted file-name.
- incrementingIntegers(OutputPatternIntegerSuffix, int, int) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
- IncrementingIntegers - Class in org.anchoranalysis.io.manifest.sequencetype
- IncrementingIntegers() - Constructor for class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
- IncrementingIntegers(int) - Constructor for class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
- IncrementingIntegers(int, int) - Constructor for class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
- incrementSumBuffer(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
-
Increments a particular offset in the sum bufffer by a certain amount
- incrementValue(int) - Method in class org.anchoranalysis.math.histogram.Histogram
- incrementValueBy(int, int) - Method in class org.anchoranalysis.math.histogram.Histogram
- incrementValueBy(int, long) - Method in class org.anchoranalysis.math.histogram.Histogram
-
long version of incrValBy
- incrementX() - Method in class org.anchoranalysis.spatial.point.Point2i
- incrementX() - Method in class org.anchoranalysis.spatial.point.Tuple3i
- incrementX(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- incrementX(int) - Method in class org.anchoranalysis.spatial.point.Point2i
- incrementX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- incrementY() - Method in class org.anchoranalysis.spatial.point.Point2i
- incrementY() - Method in class org.anchoranalysis.spatial.point.Tuple3i
- incrementY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- incrementY(int) - Method in class org.anchoranalysis.spatial.point.Point2i
- incrementY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- incrementZ() - Method in class org.anchoranalysis.spatial.point.Tuple3i
- incrementZ(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- incrementZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- incrEnergy(double) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- incrKernelAccpt(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- incrKernelProp(int) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- incrSize(double) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- incrTemperature(double) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- incrWorker() - Method in class org.anchoranalysis.core.progress.ProgressReporterMultiple
- IndependentChannels - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Converts each channel independently and creates a single-channeled stack from the conversion.
- IndependentChannels() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
- index(int) - Method in class org.anchoranalysis.plugin.io.multifile.IntegerRange
-
Maps an original integer to it's index from (0..size]
- Indexable - Class in org.anchoranalysis.core.index
-
Holds a single-index which is hashable and comparable.
- Indexable(int) - Constructor for class org.anchoranalysis.core.index.Indexable
- IndexableMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy
- IndexableMarksWithEnergy(int, MarksWithEnergyBreakdown) - Constructor for class org.anchoranalysis.mpp.feature.energy.IndexableMarksWithEnergy
- IndexableOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
An output-name with an index somehow appended or prepended in a particular style.
- IndexableOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
- IndexableOutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
- IndexableOutputNameStyle(IndexableOutputNameStyle) - Constructor for class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
-
Copy constructor
- IndexableOverlays - Class in org.anchoranalysis.overlay
- IndexableOverlays(int, OverlayCollection) - Constructor for class org.anchoranalysis.overlay.IndexableOverlays
- IndexBridge<T> - Class in org.anchoranalysis.core.index
- IndexBridge(GetterFromIndex<T>) - Constructor for class org.anchoranalysis.core.index.IndexBridge
- IndexByChannel<T> - Class in org.anchoranalysis.mpp.voxel.partition
- IndexByChannel() - Constructor for class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
- IndexByRegion<T> - Class in org.anchoranalysis.mpp.voxel.partition
- IndexByRegion(VoxelPartitionFactory<T>, int, int) - Constructor for class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
- IndexedCSVRows - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv
-
Stores the rows from the CSV file.
- IndexedCSVRows(ReadByLine, ColumnDefinition) - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.csv.IndexedCSVRows
-
Creates an index of the rows of the CSV file according to a particular columnDefinition
- IndexedRegionBase - Class in org.anchoranalysis.plugin.mpp.bean.region
-
MarkRegionwith a region and an index - IndexedRegionBase() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- IndexGettableSettable - Interface in org.anchoranalysis.core.index
- IndexGetter - Interface in org.anchoranalysis.core.index
- indexIncr(String) - Method in class org.anchoranalysis.io.generator.sequence.SequenceMemory
- indexInitialPoint() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
- indexOf(Object) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- indexOf(String) - Method in class org.anchoranalysis.feature.name.FeatureNameMapToIndex
-
The index for a particular featureName
- indexOf(Mark) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- indexOf(Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- IndexSetter - Interface in org.anchoranalysis.core.index
- IndirectlyFromListBeanFactory<T extends AnchorBean<T>,S> - Class in org.anchoranalysis.bean.xml.factory
- IndirectlyFromListBeanFactory(CheckedFunction<List<T>, S, ? extends Exception>) - Constructor for class org.anchoranalysis.bean.xml.factory.IndirectlyFromListBeanFactory
- informLatestState(T) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
-
Called every time a proposal is accepted, so a kernel can potentially keep track of the state of the current image
- informLatestState(T) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelIndependent
- init() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- init() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- init() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationCondition
- init() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
- init() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
- init(Path) - Method in class org.anchoranalysis.io.manifest.Manifest
- init(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryOutcomeImageLabeller
- init(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
- init(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller
-
Should be called once before calling any other methods
- init(Path) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
- init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.image.feature.bean.score.VoxelScore
-
Initializes the voxels-score.
- init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
- init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.FromParamsBase
- init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- init(List<Histogram>, Optional<KeyValueParams>) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
- init(List<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
- init(List<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.RemoveOverlappingObjects
- init(List<WithConfidence<BoundingBox>>) - Method in class org.anchoranalysis.plugin.image.bean.box.RemoveOverlappingBoundingBoxes
- init(List<WithConfidence<T>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
-
Called before the operation begins with all proposals
- init(BeanInstanceMap) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
- init(Logger) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.AfterCondition
- init(Logger) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.IncreaseFeatureCondition
- init(FeatureInitParams, Logger) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache
-
Initialises the cache.
- init(FeatureInitParams, Logger) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
- init(FeatureInitParams, Logger) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
- init(FeatureInitParams, Feature<T>, Logger) - Method in interface org.anchoranalysis.feature.calculate.InitializableFeature
- init(ArrangeStack, List<RGBStack>) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.RasterArranger
- init(Mask) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- init(Mask) - Method in class org.anchoranalysis.mpp.bean.points.updatable.UpdatablePointsContainer
- init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
- init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
- init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
- init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.density.DensityKernel
- init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.density.MaxDensityKernel3
- init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3Extent
- init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.DilationKernel3ZOnly
- init(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
- init(Generator<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
- init(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
- init(MPPInitParams, Logger) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.ListBoundCalculator
- init(VoxelPartitionFactory<T>, int, int, int) - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
- init(KernelBirth<T>, KernelDeath<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
-
Must be called before makeProposal
- init(P, Logger) - Method in class org.anchoranalysis.bean.initializable.InitializableBean
- init(T, Logger) - Method in interface org.anchoranalysis.bean.initializable.params.ParamsInitializer
- initBeanInstance(Object, BeanDeclaration, Object) - Method in class org.anchoranalysis.bean.xml.factory.AnchorDefaultBeanFactory
- initBeforeCalc(KernelCalculationContext) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
- initBeforeCalc(KernelCalculationContext) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelIndependent
- initBeforeCalc(KernelCalculationContext) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- InitException - Exception in org.anchoranalysis.core.exception
-
An exception that occurs when initializing something, and it doesn't succeed
- InitException(String) - Constructor for exception org.anchoranalysis.core.exception.InitException
- InitException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.InitException
- InitException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.InitException
- initHeaders(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
- initHeaders(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
- initHeaders(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
- InitializableBean<B,P extends BeanInitParams> - Class in org.anchoranalysis.bean.initializable
-
A bean that must be initialized with some parameters before being used.
- InitializableBean(PropertyInitializer<P>, PropertyDefiner) - Constructor for class org.anchoranalysis.bean.initializable.InitializableBean
- InitializableFeature<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate
-
A feature that should be initialized with
FeatureInitParams(or a sub-class) before any calculations occur. - initializePhase(int) - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
-
Initialize the next phase of the algorithm by clearing the committed workers and jobs sets and by initializing the slack arrays to the values corresponding to the specified root worker.
- initializerForMPPBeans() - Static method in class org.anchoranalysis.mpp.bean.MPPBean
-
Creates a property-initializes for MPP-Beans
- initialKernel() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- InitParamsHelper - Class in org.anchoranalysis.image.feature.session
- InitParamsWithEnergyStack - Class in org.anchoranalysis.plugin.image.task.feature
- InitParamsWithEnergyStack(EnergyStack, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
- InitParamsWithEnergyStack(ImageInitParams, EnergyStack) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
- initRecursive(Logger) - Method in class org.anchoranalysis.bean.NullParamsBean
- initRecursive(FeatureInitParams, Logger) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- initRecursive(FeatureInitParams, Logger) - Method in class org.anchoranalysis.feature.shared.SharedFeatureSet
- initRecursive(P, Logger) - Method in class org.anchoranalysis.bean.initializable.InitializableBean
-
Inits this object, and all children objects, so long as they have P Once a Bean doesn't have
P, the children are not evaluated - initRecursiveWithInitializer(PropertyInitializer<?>, Logger) - Method in class org.anchoranalysis.bean.initializable.InitializableBean
-
Initializes the bean and recursively all contained beans (who have compatible initialization requirements)
- initSource(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked
-
The value and offset for the source point (around which we process neighbors)
- initSource(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute
-
The value and offset for the source point (around which we process neighbors)
- initSource(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
- initSource(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
- initSource(Point3i, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor
-
Specify the source-point (of which all the processed points are neighbors)
- initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
- initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- initUpdatableMarkSet(MemoForIndex, EnergyStack, Logger, SharedFeatureMulti) - Method in interface org.anchoranalysis.mpp.mark.set.UpdatableMarkSet
- initWithProposerSharedObjects(MPPInitParams, Logger) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- INPUT_IMAGE - Static variable in class org.anchoranalysis.image.experiment.identifiers.StackIdentifiers
- INPUT_IMAGE_MASK - Static variable in class org.anchoranalysis.image.experiment.identifiers.StackIdentifiers
- INPUT_IMAGE_VISUAL - Static variable in class org.anchoranalysis.image.experiment.identifiers.StackIdentifiers
- InputBound<T,S> - Class in org.anchoranalysis.experiment.task
-
Input for executing a task, associated with shared-state and other parameters.
- InputBound(T, S, Manifest, boolean, InputOutputContextStateful) - Constructor for class org.anchoranalysis.experiment.task.InputBound
- InputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.io
-
SelectParam<Path>factory for inputs. - InputForMPPBean - Interface in org.anchoranalysis.mpp.io.input
-
The input can be used to initialize an MPP Bean
- inputName() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
- InputOutputContext - Interface in org.anchoranalysis.io.output.outputter
-
A context for performing input generally and outputting to a particular output-directory.
- InputOutputContextStateful - Class in org.anchoranalysis.experiment.task
-
This exists as an implementation of
InputOutputContextthat exposes aStatefulMessageLogger. - InputOutputContextStateful(ExperimentExecutionArguments, Outputter, StatefulMessageLogger, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.task.InputOutputContextStateful
- InputOutputContextSubdirectoryCache - Class in org.anchoranalysis.io.output.outputter
-
Caches a
InputOutputContextfor each subdirectory as they are created. - InputOutputContextSubdirectoryCache(InputOutputContext, ManifestDirectoryDescription, boolean) - Constructor for class org.anchoranalysis.io.output.outputter.InputOutputContextSubdirectoryCache
- InputOutputExperiment<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.io
-
An experiment that uses both an
InputManagerto specify inputs and aOutputManagerto specify outputting. - InputOutputExperiment() - Constructor for class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
- InputProcessContext<S> - Class in org.anchoranalysis.plugin.image.task.feature
- InputProcessContext(ExportFeatureResultsAdder, S, FeatureNameList, Optional<String>, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
- inputs(ImageInitParams, Logger) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
- inputs(InputManagerParams) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
- inputs(InputManagerParams) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.Shuffle
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
- inputs(InputManagerParams) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
- inputSelectParam(CommandLine, String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory
-
Can point to either: a path ending in .xml, assumed to BeanXML for an input manager a directory, set as an the inputDirectory in the input-context a string with a wild-card, assumed to be a glob, set into the input-context as a glob a string with a period and without any forward or backwards slashes, set into the input-context as an extension to match
- inputType() - Method in class org.anchoranalysis.feature.bean.Feature
-
The class corresponding to feature input-type (i.e.
- inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
- inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
- inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureOperator
- inputType() - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
- inputType() - Method in class org.anchoranalysis.feature.bean.results.FeatureResults
- inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureEnergy
- inputType() - Method in class org.anchoranalysis.image.feature.bean.FeatureHistogram
- inputType() - Method in class org.anchoranalysis.image.feature.bean.object.collection.FeatureObjectCollection
- inputType() - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeaturePairObjects
- inputType() - Method in class org.anchoranalysis.image.feature.bean.object.single.FeatureSingleObject
- inputType() - Method in class org.anchoranalysis.image.feature.bean.stack.FeatureStack
- inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
- inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureAllMemo
- inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeaturePairMemo
- inputType() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.FeatureSingleMemo
- inputType() - Method in class org.anchoranalysis.mpp.feature.bean.mark.collection.FeatureMarkCollection
- inputType() - Method in class org.anchoranalysis.mpp.feature.bean.mark.FeatureMark
- inputType() - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
- inputType() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsMark
- inputType() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
- inputTypesExpected() - Method in class org.anchoranalysis.experiment.bean.task.HelloWorld
- inputTypesExpected() - Method in class org.anchoranalysis.experiment.bean.task.Task
-
Highest class(es) that will function as a valid input.
- inputTypesExpected() - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AggregateAnnotations
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
-
Highest class(es) that will function as a valid input.
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
- inputTypesExpected() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
- InputTypesExpected - Class in org.anchoranalysis.experiment.task
-
A list of base (parent) classes for input-types that a task expects
- InputTypesExpected(Class<? extends InputFromManager>) - Constructor for class org.anchoranalysis.experiment.task.InputTypesExpected
- insertAfter(List<Point3i>) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
-
Inserts points at end of existing path.
- insertBefore(List<Point3i>) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
-
Inserts points before existing path.
- insertBeginning(String) - Method in class org.anchoranalysis.feature.name.FeatureNameList
-
Inserts a new feature-name at the beginning of the list
- insertBeginning(String[]) - Method in class org.anchoranalysis.feature.name.FeatureNameList
-
Inserts new feature-names at the beginning of the list
- InsertRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Generates an out string where $digit$ is replaced with the #digit group from a regex
- InsertRegExGroups() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
- InsertRegExGroups(RegEx, String) - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
- InsideBoxOn - Class in org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
-
Creates a binary img-channel where all pixels are 'on' within a certain x, y, z coordinate range
- InsideBoxOn() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
- inSlices - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
- instance - Static variable in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
- instance() - Static method in class org.anchoranalysis.bean.initializable.params.NullInitParams
- instance() - Static method in class org.anchoranalysis.feature.input.FeatureInputNull
- instance() - Static method in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
- instance() - Static method in class org.anchoranalysis.image.core.channel.factory.ChannelFactory
-
Singleton
- instance() - Static method in class org.anchoranalysis.image.voxel.factory.VoxelsFactory
-
Singleton
- instance() - Static method in class org.anchoranalysis.io.bioformats.ConfigureBioformatsLogging
- instance() - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMapSingleton
- instance() - Static method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeNull
- instance() - Static method in class org.anchoranalysis.plugin.io.input.path.RootPathMap
- INSTANCE - Static variable in class org.anchoranalysis.experiment.task.NoSharedState
- INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
- INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType
- INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType
- INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedIntVoxelType
- INSTANCE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType
- INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.All
-
A singleton instance of
All. - INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.IgnoreUnderscorePrefix
-
A singleton instance of
IgnoreUnderscorePrefix. - INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.enabled.None
-
A singleton instance of
None. - INSTANCE - Static variable in class org.anchoranalysis.io.output.bean.rules.Permissive
-
A singleton instance of
Permissive. - InsufficientPointsException - Exception in org.anchoranalysis.mpp.bean.points.fitter
- InsufficientPointsException() - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException
- InsufficientPointsException(String) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException
- InsufficientPointsException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException
- InsufficientPointsException(Throwable) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.InsufficientPointsException
- IntBinaryOperation - Interface in org.anchoranalysis.core.functional.checked
-
A binary operation on two int-values that produces an int
- IntegerRange - Class in org.anchoranalysis.plugin.io.multifile
- IntegerRange(int) - Constructor for class org.anchoranalysis.plugin.io.multifile.IntegerRange
- IntegerRange(int, int) - Constructor for class org.anchoranalysis.plugin.io.multifile.IntegerRange
- IntegerSequenceContaner - Class in org.anchoranalysis.core.index.bounded
- IntegerSequenceContaner(int) - Constructor for class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
- integerSet() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- IntegerSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
-
Outputs a file-name involving an integer of length
numberDigitswith leading zeros. - IntegerSuffixOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
- IntegerSuffixOutputNameStyle(String, int) - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
- IntegerSuffixOutputNameStyle(String, String, int) - Constructor for class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
- Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Calculates a statistic from the intensity values covered by a single object-mask in a channel.
- Intensity - Class in org.anchoranalysis.plugin.image.feature.bean.stack.intensity
-
The intensity of a particular channel of the stack, by default the mean-intensity.
- Intensity - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
- Intensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
- Intensity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
- Intensity() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
- IntensityGradientBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
- IntensityGradientBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
- IntensityGreaterEqualThan - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Only keep objects where at least one voxel (on a particular channel) has intensity greater or equal to a threshold.
- IntensityGreaterEqualThan() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
- intensityMax(Voxels<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
-
Finds the maximum intensity-value (as an int) among all voxels.
- IntensityMeanCalculator - Class in org.anchoranalysis.plugin.image.intensity
- IntensityMeanMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
- IntensityMeanMaxSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
- IntensityMeanShell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Constructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shell
- IntensityMeanShell() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShell
- IntensityMeanShellBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Constructs a shell around an object-mask using a standard dilation and erosion process
- IntensityMeanShellBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
- IntensityMeanShellMaxSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
Constructs a 'shell' around an object by a number of dilation/erosion operations (not including the original object-mask) and measures the mean intensity of this shell
- IntensityMeanShellMaxSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellMaxSlice
- interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in interface org.anchoranalysis.image.voxel.interpolator.Interpolator
-
Interpolates from
voxelsSourcetovoxelsDestinationfor unsigned 8-bit buffers. - interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2
- interpolateByte(VoxelBuffer<UnsignedByteBuffer>, VoxelBuffer<UnsignedByteBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorNone
- interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in interface org.anchoranalysis.image.voxel.interpolator.Interpolator
-
Interpolates from
voxelsSourcetovoxelsDestinationfor unsigned 16-bit buffers. - interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2
- interpolateShort(VoxelBuffer<UnsignedShortBuffer>, VoxelBuffer<UnsignedShortBuffer>, Extent, Extent) - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorNone
- InterpolateUtilities - Class in org.anchoranalysis.image.voxel.interpolator
- Interpolator - Interface in org.anchoranalysis.image.voxel.interpolator
- InterpolatorBean - Class in org.anchoranalysis.image.bean.interpolator
- InterpolatorBean() - Constructor for class org.anchoranalysis.image.bean.interpolator.InterpolatorBean
- InterpolatorBeanImageJ - Class in org.anchoranalysis.plugin.imagej.bean.interpolator
- InterpolatorBeanImageJ() - Constructor for class org.anchoranalysis.plugin.imagej.bean.interpolator.InterpolatorBeanImageJ
- InterpolatorFactory - Class in org.anchoranalysis.image.voxel.interpolator
- InterpolatorImgLib2 - Class in org.anchoranalysis.image.voxel.interpolator
-
Performs interpolation using ImgLib2
- InterpolatorImgLib2(InterpolatorFactory<UnsignedByteType, RandomAccessible<UnsignedByteType>>, InterpolatorFactory<UnsignedShortType, RandomAccessible<UnsignedShortType>>) - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2
- InterpolatorImgLib2Lanczos - Class in org.anchoranalysis.image.voxel.interpolator
- InterpolatorImgLib2Lanczos() - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2Lanczos
- InterpolatorImgLib2Linear - Class in org.anchoranalysis.image.voxel.interpolator
- InterpolatorImgLib2Linear() - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2Linear
- InterpolatorImgLib2NearestNeighbor - Class in org.anchoranalysis.image.voxel.interpolator
- InterpolatorImgLib2NearestNeighbor() - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2NearestNeighbor
- InterpolatorNone - Class in org.anchoranalysis.image.voxel.interpolator
-
Doesn't do any interpolation, just copies values
- InterpolatorNone() - Constructor for class org.anchoranalysis.image.voxel.interpolator.InterpolatorNone
- intersect(ObjectMask, Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Intersects this object-mask with another
- IntersectingCircleObjectsFixture - Class in org.anchoranalysis.test.feature.plugins.objects
- intersection() - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
For evaluating the intersection between this bounding-box and others
- Intersection - Class in org.anchoranalysis.plugin.image.bean.object.match
- Intersection - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair
-
Finds the intersection of two objects and calculates a feature on it
- Intersection() - Constructor for class org.anchoranalysis.plugin.image.bean.object.match.Intersection
- Intersection() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
- IntersectionOverUnion - Class in org.anchoranalysis.plugin.image.box
-
Calculates the intersection-over-union score a pair of bounding-boxes.
- intersectsWith(ObjectMask) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
-
All objects that intersect with another object.
- intersectsWith(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
- intersectsWith(BoundingBox) - Method in class org.anchoranalysis.spatial.rtree.RTree
- IntersectsWith - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Keeps objects which intersects with ANY ONE of a collection of other objects.
- IntersectsWith() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
- intersectsWithAsIndices(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
- IntersectsWithContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
-
Returns only the objects that intersect with at least one object in the container
- IntersectsWithContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
- intersectWith(Extent) - Method in class org.anchoranalysis.spatial.Extent
-
Intersects this extent with another (i.e.
- intFromDoubleCeil(Point3d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- intFromDoubleFloor(Point2d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- intFromDoubleFloor(Point3d) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- intFromFloat(Point3f, boolean) - Static method in class org.anchoranalysis.spatial.point.PointConverter
- INVALID_AXIS_INDEX - Static variable in class org.anchoranalysis.spatial.axis.AxisTypeConverter
- INVALID_AXIS_STRING - Static variable in class org.anchoranalysis.spatial.axis.AxisTypeConverter
- invalidate() - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache
-
Invalidates existing caches so all calculations occur freshly
- invalidate() - Method in interface org.anchoranalysis.feature.calculate.cache.ResettableCalculation
-
Resets the cached-calculation, so the next call to doOperationWithParams() is guaranteed to calculation the operation, and store the value in the cache.
- invalidate() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculation
- invalidate() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
-
Invalidates the cache, removing any items already stored.
- invalidate() - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
- invalidate() - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
- invalidateExcept(Set<ChildCacheName>) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSessionCache
-
Invalidates existing caches so all calculations occur freshly - except some particular child-caches who are not invalidated
- invalidateExcept(Set<ChildCacheName>) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalCalculationCache
- invalidateExcept(Set<ChildCacheName>) - Method in class org.anchoranalysis.feature.session.cache.horizontal.HorizontalFeatureCache
- InvalidPathArgumentException - Exception in org.anchoranalysis.launcher.executor.selectparam.path
-
An exception throw if an invalid-path is inputted as an argument.
- InvalidPathArgumentException(String, InvalidPathException) - Constructor for exception org.anchoranalysis.launcher.executor.selectparam.path.InvalidPathArgumentException
- invert() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
-
Changes the OFF state to be the ON state and vice-versa.
- invert() - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
- invert() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Produces a new object-mask that uses the same voxel-buffer but inverts the OFF and ON
- invert() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
- invert(Mask) - Static method in class org.anchoranalysis.image.core.mask.MaskInverter
-
Modifies a mask so that OFF voxels become ON voxels and vice versa
- Invert - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Subtracts each voxel from the maximum value for the channel's data type (e.g.
- Invert - Class in org.anchoranalysis.plugin.image.bean.mask.provider
-
Switches on voxels to off and vice-versa.
- Invert - Class in org.anchoranalysis.plugin.image.bean.segment.binary
-
Performs a segmentation and inverts and ON and OFF bytes
- Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.Invert
- Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
- Invert() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Invert
- InvertedMax<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
-
Finds the repciprocal (multiplicate inverse), but imposes a maximum ceiling via a constant.
- InvertedMax() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
- invertObjectDuplicate(ObjectMask) - Static method in class org.anchoranalysis.image.core.mask.MaskInverter
-
Creates a new object-mask where OFF voxels become ON voxels and vice versa
- isAccepted() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
- isAccepted() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
- isAccepted() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- isAcceptNoResolution() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
- isAcceptOutsideScene() - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
- isAddName() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- isAddOne() - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
- isApplyResolution() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
-
Multiples the values by the x-resolution, if it exists.
- isAsPercentage() - Method in class org.anchoranalysis.feature.bean.results.Quantile
-
If true, the quantile is interpreted as a percentage rather than a decimal
- isAtLeastOnePositive() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
-
Checks that at least one of
iterationsDilationanditerationsErosionis more than 0 - isAvoidBulletOnFirst() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
-
Iff true no bullet is added for the very first-item in the list
- isAvoidDivideByZero() - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
- isAvoidOverlappingObjects() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
-
If true, no overlapping objects are treated as pairs
- isBest() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- isBest() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- isBigNeighborhood() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
-
iff true uses a big-neighborhood (8 or 26 connectivity) for dilation
- isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
- isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
-
If true uses 8 neighborhood rather than 4 neighborhood etc.
- isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
-
if true, uses 8 neighborhood instead of 4, and similarly in 3d
- isBigNeighborhood() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
- isBigNeighborhood() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
- isBit0() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- isBit1() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- isBit2() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- isBit3() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- isBit4() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- isBit5() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- isBit6() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- isBit7() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderBase
- isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderXY
- isBoundingBoxAtBorder(BoundingBox, Extent) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.AtBorderZ
- isBySlices() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
- isCalledRegisterAllPackage() - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories
- isCellUsed(int, int) - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
- isChangeExisting() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase
-
If true, the existing channel can be changed.
- isClearOutsideMask() - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
- isClosed() - Method in class org.anchoranalysis.spatial.Contour
- isCollapseFilename() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
- isCompatibleWith(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType
-
Can these parameters be used with a particular feature?
- isCompatibleWith(Mark) - Method in interface org.anchoranalysis.mpp.mark.CompatibleWithMark
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.EllipseBoundsCheck
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.Not
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceAbstractPosition
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceRadii
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.CreateNew
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.UniformRandom
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomXY
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelReplacePartition
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ConstantWeight
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.NumberPoints
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
- isCompatibleWith(Mark) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
- isCompleted() - Method in class org.anchoranalysis.experiment.task.processor.JobState
- isCompletedFailure() - Method in class org.anchoranalysis.experiment.task.processor.JobState
- isCompletedSuccessfully() - Method in class org.anchoranalysis.experiment.task.processor.JobState
- isConditionTrue() - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
- isConnectedComponentID(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
- isConnectedComponentIDCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- isConnectedComponentIDCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
- isConsiderForMerge() - Method in class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
- isConvexHull() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
-
If true, Reduces the set of points by applying a convex-hull operation
- isCov() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
- isCreateShort() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
- isCreateShort() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
- isCreateShort() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
- isCreateShort() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
-
If True creates an unsigned short-image
- isCsvIgnoreZeros() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
-
Iff true, bins with zero-counts are not written as a row in the CSV file.
- isDatasetNameSubdirectory() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
If true the datasetName is appended as a subdirectory e.g.
- isDay() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
-
If true, the current day (yyyy.MM.dd) is included in the output
- isDebug() - Method in class org.anchoranalysis.bean.shared.path.RootPath
-
If true this root is preferred, when executing a job in debugging mode
- isDebug() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
- isDebugEnabled() - Method in class org.anchoranalysis.experiment.task.InputOutputContextStateful
- isDebugEnabled() - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
-
Is debug-mode enabled?
- isDebugEnabled() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
- isDebugMode() - Method in class org.anchoranalysis.io.output.path.prefixer.FilePathPrefixerContext
- isDebugModeEnabled() - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
- isDefault() - Method in class org.anchoranalysis.launcher.executor.selectparam.path.CustomManagerFromPath
- isDefault() - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam
-
Is this the default option that occurs without any additional user effort?
- isDefault() - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
- isDetailedLogging() - Method in class org.anchoranalysis.experiment.task.InputBound
- isDetailedLogging() - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
-
Iff true, additional log messages are written to describe each job in terms of its unique name, output folder, average execution time etc.
- isDifferentColorsForMatches() - Method in class org.anchoranalysis.annotation.io.assignment.generator.ColorPool
- isDirect() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
-
Is this buffer direct or non-direct?
- isDirect() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
-
Is this buffer direct or non-direct?
- isDirectionChainCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- isDirectionChainCode(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
- isDisableDebugMode() - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
- isDisableDebugMode() - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
- isDisablePathModification() - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationWriter
- isDo3D() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
- isDo3D() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
- isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
-
Whether to perform the morphological dimensions in 3D or 2D
- isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
- isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
- isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
- isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
- isDo3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
- isDo3D() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
- isDummyMode() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- isDuplicate() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting existing data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- isDuplicate() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- isEmpty() - Method in interface org.anchoranalysis.bean.StringBeanCollection
- isEmpty() - Method in class org.anchoranalysis.bean.StringList
- isEmpty() - Method in class org.anchoranalysis.bean.StringSet
- isEmpty() - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider
-
Are there any items in the provider
- isEmpty() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- isEmpty() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
- isEmpty() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- isEmpty() - Method in class org.anchoranalysis.image.core.stack.TimeSequence
- isEmpty() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- isEmpty() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
-
If no output-names exist.
- isEmpty() - Method in class org.anchoranalysis.math.histogram.Histogram
- isEmpty() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- isEmpty() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- isEmpty() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
- isEmpty() - Method in class org.anchoranalysis.spatial.box.PointRange
-
Has a valid min and max defined? In other words, has at least one point been added?
- isEmpty() - Method in class org.anchoranalysis.spatial.Extent
- isEnabled() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput
- isErodeAtBoundary() - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
- isErrorDisconnectedObjects() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
-
If true, throws an error if there is a disconnected object after the erosion
- isEvaluated() - Method in class org.anchoranalysis.core.cache.CachedSupplierBase
- isExceptionIfEmpty() - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
-
If true, then an exception is thrown if the histogram is empty, otherwise
is returned. - isExcludeZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
-
Iff true, zero-valued voxels are excluded from the histogram
- isExcludeZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
- isExcludeZero() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
-
If true, zeros are excluded from considering in the histogram
- isExecuting() - Method in class org.anchoranalysis.experiment.task.processor.JobState
- isExitBeforeOptimization() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Iff true the algorithm exits before optimization begins (useful for debugging).
- isExitWithMinima() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
-
If true, exits early and just returns the minima, without any further segmentation
- isExtendInZ() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
-
Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all slices)
- isFindMaxima() - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
-
If true, the maxima of the score is searched for.
- isFinished() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
- isFirst() - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
-
Iff true, first object is used, otherwise the second
- isFirstLineHeaders() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- isFixRandomSeed() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Iff true uses a constant seed for the random-number-generator (useful for debugging).
- isFlatten() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
-
If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make it 2D
- isFlatten() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
-
If true, objects and the background are flattened in the z dimension (via maximum intensity projection), so that a 2D image is produced
- isForceBinary() - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- isForceChangeBytes() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
-
If true, rather than modifying the binary-values (an index) bytes are modified in the buffer to reflect the existing binary-values.
- isForceDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
-
Whether more detailed log-messages around each experiment occur.
- isForceEagerEvaluation() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- isForceRGB() - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
-
If set, ensures every stack is converted into 3 channels
- isForwardDirectionOnly() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- isGaussian() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
-
If true, the Gaussian filter is included
- isGPU() - Method in class org.anchoranalysis.core.concurrency.WithPriority
- isHighestTwoRadiiOnly() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
- isIgnoreAtThreshold() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
- isIgnoreAtThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
- isIgnoreCase() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
- isIgnoreFileNotFoundAppend() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- isIgnoreFittingFailure() - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
-
If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply not included (with only a log error) If false, an exception is thrown
- isIgnoreHidden() - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
- isIgnoreHigherSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
- isIgnoreLowerSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
- isIgnoreMissingChannel() - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
-
Iff true and we cannot find a channel in the file, we ignore it and carry on
- isIgnoreNaN() - Method in class org.anchoranalysis.feature.bean.operator.Sum
-
If true, we ignore any NaN values.
- isIgnoreNoObjects() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
-
If true, then the outputs (outline, mask, image etc.) are not written for images that produce no objects.
- isIgnoreRangeAxisOutside() - Method in class org.anchoranalysis.plot.index.LinePlot
- isIgnoreZero() - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
- isIncludeFeatureNames() - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
-
If true, the names of the imageFeatures are taken as a combination of the namedItem and the actual features
- isIncludeFileName() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
- isIncludeFirst() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
-
Include features for the First-object of the pair
- isIncludeFolders() - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
-
If false, the folders are ignored, and only the file-name is used in the output
- isIncludeMerged() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
-
Include features for the Merged-object of the pair
- isIncludeSecond() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
-
Include features for the Second-object of the pair
- isIncludeShell() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
- isIncludeZ() - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
- isInitialized() - Method in class org.anchoranalysis.bean.initializable.InitializableBean
- isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
-
Is an input-object compatible with this particular task?
- isInputCompatibleWith(Class<? extends InputFromManager>) - Method in class org.anchoranalysis.experiment.bean.task.Task
-
Is an input-object compatible with this particular task?
- isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
- isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
- isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
- isInteger() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
- isInterpolate() - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
- isInverse() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
- isInverse() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
-
Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is removed)
- isInverseMask() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
- isInvert() - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
- isInvert() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
- isInvert() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.EnsureRegExMatch
-
Iff true, then a file is rejected if regEx matches and vice-versa (opposite to normal behaviour)
- isInvertDecisionValue() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
- isItemIncluded(T) - Method in class org.anchoranalysis.plot.bean.Plot
-
Whether to include this particular item in the plot?
- isKeepEntireImage() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
-
If true, rather than writing out a bounding-box around the object-mask, the entire image is written
- isKeepExtremes() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
- isKeepZ() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
-
Keep the z-resolution if it is already defined
- isKeyRequired() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- isLabel() - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
-
If true a label is added beside every image showing the slice index
- isLeaf() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- isLogPath() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
-
if true, the pathIn and pathOut are logged.
- isMarksSpan() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- isMarksSpan(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- isMarksSpan(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
- isMax() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- isMedian() - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
-
If true, the median filter is included
- isMemberFlag(byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
- isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd
- isMemberFlag(byte, byte) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipOr
- isMemberFlagAnd(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
- isMemberFlagOr(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
- isMerge() - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
- isMinima(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
- isMinima(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- isMip() - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
- isMip() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
- isMip() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMIPBase
- isNeighborVoxelAccepted(Point3i, int, int, int, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhood
- isNeighborVoxelAccepted(Point3i, int, int, int, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
- isNeighborVoxelAccepted(Point3i, int, int, int, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodIgnoreOutsideScene
- isNeighborVoxelAccepted(Point3i, int, int, int, Extent) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask
- isNewValuesPossible() - Method in interface org.anchoranalysis.image.voxel.interpolator.Interpolator
-
Returns true if it's possible for values to be created after interpolation that aren't found in the input-image.
- isNewValuesPossible() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2Lanczos
- isNewValuesPossible() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2Linear
- isNewValuesPossible() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorImgLib2NearestNeighbor
- isNewValuesPossible() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorNone
- isNoBlack() - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
- isNormalize() - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
- isNormalize() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZOverlapRatio
- isNormalizeFeatures() - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
-
Normalize features
- isNoScale() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
-
If the scale-factor involves no scaling at all
- isNumeric() - Method in class org.anchoranalysis.core.value.TypedValue
- isNumeric() - Method in class org.anchoranalysis.io.output.bean.ReportFeature
- isNumeric() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
- isNumeric() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
- isNumeric() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
- isNumeric() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
- isNumeric() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.NumberMarksFromManifest
- isNumeric() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
- isNumeric() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
- isOff(byte) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
- isOff(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
- isOff(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
- isOn() - Method in interface org.anchoranalysis.io.generator.sequence.OutputSequence
- isOn() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing
- isOn() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed
- isOn(byte) - Method in class org.anchoranalysis.image.voxel.binary.values.BinaryValuesByte
- isOn(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
- isOn(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
- isOutline() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
-
If true, an outline is drawn around the entries.
- isOutlineAtBoundary() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
- isOutputCSV() - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
-
Iff true, a mapping.csv file is created showing the mapping between the original-names and the anonymized versions
- isOutputEnabled() - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
- isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.All
- isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.IgnoreUnderscorePrefix
- isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.None
- isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
- isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
- isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
- isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
- isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
- isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary
- isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelInSet
- isOutputEnabled(String) - Method in class org.anchoranalysis.io.output.enabled.single.SingleLevelNot
- isOutputEnabled(String) - Method in interface org.anchoranalysis.io.output.enabled.single.SingleLevelOutputEnabled
-
Is a particular a particular output-enabled?
- isOutputShort() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
-
Iff true, outputs a short channel, otherwise byte channel
- isOutsideAtThreshold() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
- isOutsideAtThreshold() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
- isOutsideAtThreshold() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
- isOutsideAtThreshold() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
- isParamPrefixAppendNumber() - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
-
If true the constant is appended to the param prefix (a dot and a number)
- isPhysical() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
- isPlateau(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
- isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
- isPlayloadUsed() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
-
Is the payload considered in making decisions? (iff false, payload of nodes is irrelvant)
- isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
- isPointConvexTo(Point3i, Point3i, BinaryVoxels<UnsignedByteBuffer>, boolean) - Static method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
- isPointInside(DrawOverlay, Point3i) - Method in class org.anchoranalysis.mpp.overlay.OverlayMark
- isPointInside(DrawOverlay, Point3i) - Method in class org.anchoranalysis.overlay.object.OverlayObjectMask
- isPointInside(DrawOverlay, Point3i) - Method in class org.anchoranalysis.overlay.Overlay
-
Is a point inside an overlay? (for a particular OverlayWriter).
- isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.Mark
- isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.PointList
- isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
- isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
- isPointInside(Point3d) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
- isPointOn(Point3i) - Method in class org.anchoranalysis.image.core.mask.Mask
- isPointOnMask(Point3d, EnergyStack, Function<Point3d, Point3i>) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
- isPrefix() - Method in class org.anchoranalysis.bean.define.adder.FromXmlList
-
If true, a prefix is prepended to the name of each added bean.
- isPreserveExtensionIfDuplicate() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
-
Keeps the extension if the file-name (without the extension) becomes duplicated with another
- isPreventObjectIntersection() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
-
Iff true, objects can only be neighbors if they have no intersecting voxels.
- isProposal() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
- isProposed() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
- isRadiusInMeters() - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
- isRecordedAsEnabled(String) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
-
Is a particular output-name recorded as enabled?
- isRecurseSubfolders() - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
- isRecursive() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
Whether to apply the search recursively or not
- isRejectIterationIfAllLow() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
- isRejectIterationIfDisconnected() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
- isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.EqualTo
- isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.GreaterThan
- isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.GreaterThanEqualTo
- isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.LessThan
- isRelationToValueTrue(double, double) - Method in class org.anchoranalysis.math.relation.LessThanEqualTo
- isRelationToValueTrue(double, double) - Method in interface org.anchoranalysis.math.relation.RelationToValue
- isRemoveExtensionInDescription() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
-
Whether to remove the file-extension from the filename.
- isRemoveTouchingBorderXY() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
- isReplaceMatchesWithSolids() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- isReplaceWithMidpoint() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
- isReportFitterErrors() - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
- isRequireAllFilesMatch() - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- isRequireBBoxNeighbors() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
-
Requires for any potential merge that the bounding-boxes of the two objects must intersect or touch
- isRequireTouching() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
-
Requires the object-masks to touch.
- isResultUnusual(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceInfinity
- isResultUnusual(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceNaN
- isResultUnusual(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
- isRewardHigherSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
-
Treat the higher side as if it's the the fill cdf
- isRewardLowerSide() - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
- isRgb() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
-
If true, the output contains three channels (the input and two duplicates) instead of one
- isRGB() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- isRGB() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
- isRGB() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
- isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
- isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
- isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
- isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
- isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
-
Is it an image with three channels (red, green and blue)?
- isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
- isRGB(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.SwitchChannelTime
- isRootInStructure() - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
If true the directory structure is ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
- isRotateOnlyIn2DPlane() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
- isSecond() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
-
Only relevant if time==true.
- isSecondary() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
-
If
proposalis true, this toggles between the primary and secondary proposal - isSelective() - Method in class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
-
Whether the output should be checked to see if it is allowed or not.
- isShowAgg() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
- isShowBest() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
- isShowDomainAxis() - Method in class org.anchoranalysis.plot.index.BarPlot
- isShowVerticalAxisLines() - Method in class org.anchoranalysis.plot.PlotInstance
- isSigmaInMeters() - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
- isSilentlyDeleteExisting() - Method in class org.anchoranalysis.io.output.bean.OutputManager
-
Whether to silently first delete any existing output at the intended path, or rather throw an error.
- isSilentlyDeleteExisting() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- isSkipAtBorder() - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
-
If true we do not fill any objects that touch the border
- isSkipFileName() - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
-
Iff true the filename is not considered, only the subdirectories.
- isSkipFileName() - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
- isSkipMissingChannels() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- isSlicesSeparately() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.FitBoxToOnVoxels
- isStackAsChannel() - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
-
If true, a raster-stack is treated as a single-channel, even if multiple exist (and no additionalChannel is set)
- isStackBackground() - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
- isStrongEdgeEnhancer() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
-
Enables the StrongEdgeEnhancer diffusion function
- isSubtractFromMaskOnly() - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
- isSuppress3D() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
- isSuppress3D() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
- isSuppress3D() - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
- isSuppressErrors() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- isSuppressExceptions() - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
- isSuppressExceptions() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
- isSuppressExceptions() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- isSuppressExceptions() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- isSuppressOutlineZ() - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
-
if true, the outline is suppressed in the z-dimension i.e.
- isSuppressRes() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
- isSuppressRootOut() - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
-
if true, the root is not added to the outFilePath, and the path is instead localized against the location of the BeanXML.
- isSuppressSeries() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
-
If true, the series index is not included in the outputted file-names.
- isSuppressSubfolders() - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
- isSuppressZ() - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
- isSuppressZ() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
- isSuppressZ() - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
- isSuppressZ() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
- isSuppressZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
- isSuppressZ() - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
-
If true co-voariance is suprpessed in z-dimension
- isSuppressZ() - Method in class org.anchoranalysis.plugin.mpp.bean.check.CenterOnMask
- isSuppressZ() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.UniformRandom
- isSuppressZ() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
- isSuppressZ() - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
-
Iff true, surpresses covariance in the z-direction.
- isSuppressZCovariance() - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
- isSuppressZCovariance() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
- isTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
- isTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- isTestBothDirections() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
-
iff true each combination of neighbors is tested only once, otherwise twice
- isThrowExceptionForInsufficientPoints() - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
- isThumbnailsEnabled() - Method in class org.anchoranalysis.plugin.image.task.feature.InputProcessContext
- isTime() - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
-
If true, the current time (HH.mm.ss) is included in the output
- isTransposed() - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- isUnbounded() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
- isUnboundedAtBothEnds() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
- isUnboundedOrOutsideRange(double) - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
- isUnboundedOrOutsideRangeAtBothEnds(double) - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
- isUniformlySized() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
- isUniformTyped() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
- isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
- isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
- isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
- isUnsigned() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
- isUnstarted() - Method in class org.anchoranalysis.experiment.task.processor.JobState
- isUnvisited(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
- isUnvisited(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- isUseLastSeriesIndexOnly() - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
- isUseLastSeriesIndexOnly() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
- isUseMax() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatio
- isUseMax() - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatioMask
- isUseMIP() - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
- isUseMIP() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- isUseZ() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
- isUseZ() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
- isUseZ() - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
- isVaryColors() - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
-
If true the colors change for different objects in the image (using a default color set).
- isZOnly() - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
- iterateBins(Histogram.BinConsumer) - Method in class org.anchoranalysis.math.histogram.Histogram
-
Calls
consumerfor every bin-value, increasing from min to max. - iterateBinsUntil(int, Histogram.BinConsumer) - Method in class org.anchoranalysis.math.histogram.Histogram
-
Calls
consumerfor every bin-value until a limit, increasing from min to limit (inclusive). - iterateMap(Map<K, V>, CheckedBiConsumer<K, V, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate
-
Iterate through all entries in a
Map. - iterateOverSlices(Consumer<VoxelBuffer<T>>) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
-
Calls
sliceConsumeronce for each slice with the respective buffer - iterateOverSlicesAndOffsets(ProcessVoxelBufferUnary<T>) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
-
Calls
processfor each offset in each slice - iterateOverXY(OffsettedScalarTwoDimensionalConsumer<E>) - Method in class org.anchoranalysis.spatial.Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverXY(PointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverXYOffset(CheckedIntConsumer<E>) - Method in class org.anchoranalysis.spatial.Extent
-
Calls processor once for each x and y-values but only passing an offset.
- iterateOverXYOffset(OffsettedPointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.Extent
-
Calls processor once for each x and y-values in the range.
- iterateOverXYWithShift(Point2i, PointTwoDimensionalConsumer) - Method in class org.anchoranalysis.spatial.Extent
-
Calls processor once for each x and y-values in the range, with a shift added.
- iterateOverZ(CheckedIntConsumer<E>) - Method in class org.anchoranalysis.spatial.Extent
-
Calls processor once for each z-value in the range
- iterateOverZUntil(IntPredicate) - Method in class org.anchoranalysis.spatial.Extent
-
Calls processor once for each z-value in the range unless
indexPredicatereturns false. - IterateVoxelsAll - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over all voxels in one or more
Voxels. - IterateVoxelsBoundingBox - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over the subset of image voxels within a bounding-box.
- IterateVoxelsEqualTo - Class in org.anchoranalysis.image.voxel.iterator
-
Like
IterateVoxelsAllbut specifically for equal-to operations onVoxelsof typeUnsignedByteBuffer. - IterateVoxelsIntersectingBounded - Class in org.anchoranalysis.image.voxel.iterator.intersecting
-
Like
IterateVoxelsBoundingBoxbut specifically for processing areas of intersection betweenBoundedVoxelsof typeUnsignedByteBuffer. - IterateVoxelsMask - Class in org.anchoranalysis.image.core.mask
-
Utilities for iterating over the subset of voxels corresponding to an on state in a
Mask. - IterateVoxelsNeighbors - Class in org.anchoranalysis.image.voxel.iterator.neighbor
-
Utilities for iterating over the neighboring voxels to a given point.
- IterateVoxelsObjectMask - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over the subset of voxels corresponding to an on state in an
ObjectMask. - IterateVoxelsObjectMaskOptional - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over the subset of voxels corresponding to an on state in an optional
ObjectMask. - IterateVoxelsRemaining - Class in org.anchoranalysis.image.voxel.iterator
-
Utilities for iterating over remaining voxels in one or more
VoxelBuffers. - iterator() - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
-
An iterator for each element in the sequence
- iterator() - Method in class org.anchoranalysis.bean.StringList
- iterator() - Method in class org.anchoranalysis.bean.StringSet
- iterator() - Method in class org.anchoranalysis.core.color.ColorList
- iterator() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
- iterator() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- iterator() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- iterator() - Method in class org.anchoranalysis.feature.io.name.CombinedName
- iterator() - Method in class org.anchoranalysis.feature.io.name.SimpleName
- iterator() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
- iterator() - Method in class org.anchoranalysis.feature.name.FeatureNameList
- iterator() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
- iterator() - Method in class org.anchoranalysis.feature.session.strategy.child.CacheTransferSourceCollection
- iterator() - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
- iterator() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
- iterator() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
- iterator() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- iterator() - Method in class org.anchoranalysis.image.core.stack.Stack
- iterator() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
- iterator() - Method in class org.anchoranalysis.image.core.stack.TimeSequence
- iterator() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- iterator() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
- iterator() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- iterator() - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeSet
- iterator() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- iterator() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- iterator() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- iterator() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
- iterator() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- iterator() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- iterator() - Method in class org.anchoranalysis.overlay.OverlayProperties
- iterator() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroupList
- iterator() - Method in class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
- iterator() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
- iterator() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
- iteratorCoupledManifests() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
- iteratorCoupledManifestsFor(Manifest) - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
- iteratorExperimentalManifests() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
J
- JobDescription - Class in org.anchoranalysis.experiment.task.processor
- JobDescription(String, int) - Constructor for class org.anchoranalysis.experiment.task.processor.JobDescription
- jobDirectory() - Static method in class org.anchoranalysis.io.manifest.finder.match.DirectoryMatch
- JobExecutionException - Exception in org.anchoranalysis.experiment
-
An exception that occurs when a job is executed.
- JobExecutionException(String) - Constructor for exception org.anchoranalysis.experiment.JobExecutionException
- JobExecutionException(String, Throwable) - Constructor for exception org.anchoranalysis.experiment.JobExecutionException
-
A string message displayed to the user as well as a stack-trace of the cause
- JobExecutionException(Throwable) - Constructor for exception org.anchoranalysis.experiment.JobExecutionException
- JobProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor
-
Processes a job
- JobProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.JobProcessor
- JobRootDirectory - Class in org.anchoranalysis.io.manifest.directory
-
The root directory for where outputs for a particular experiment occur.
- JobRootDirectory() - Constructor for class org.anchoranalysis.io.manifest.directory.JobRootDirectory
- JobStartStopLogger - Class in org.anchoranalysis.experiment.task.processor
-
Logs events when jobs start and stop, with or without errors.
- JobStartStopLogger(String, ConcurrentJobMonitor, boolean, int, Optional<MessageLogger>) - Constructor for class org.anchoranalysis.experiment.task.processor.JobStartStopLogger
-
Creates a job-logger.
- JobState - Class in org.anchoranalysis.experiment.task.processor
- JobState() - Constructor for class org.anchoranalysis.experiment.task.processor.JobState
- JoinRegExGroups - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Generates an outstring of the form
- JoinRegExGroups() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
K
- Kernel - Class in org.anchoranalysis.image.voxel.kernel
- Kernel<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel
-
Modifies an Object by applying a kernel
- Kernel() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
- Kernel(int) - Constructor for class org.anchoranalysis.image.voxel.kernel.Kernel
- kernelAccepted(Kernel<S>, Optional<T>, T, TransformationContext) - Method in interface org.anchoranalysis.plugin.mpp.segment.kernel.updater.KernelUpdater
-
Informs that a proposal from a particular kernel has been accepted
- kernelAccepted(Kernel<S>, Optional<T>, T, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.kernel.updater.KernelUpdaterSimple
- kernelAssigner() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
- KernelAssigner<S,T> - Interface in org.anchoranalysis.mpp.segment.kernel
- KernelAssignerAddErrorLevel<S,T> - Class in org.anchoranalysis.plugin.mpp.segment.kernel.assigner
- KernelAssignerAddErrorLevel(KernelAssigner<S, T>, ErrorNode) - Constructor for class org.anchoranalysis.plugin.mpp.segment.kernel.assigner.KernelAssignerAddErrorLevel
- KernelAssignerCalculateEnergyFromKernel<S,T> - Class in org.anchoranalysis.plugin.mpp.segment.kernel.assigner
- KernelAssignerCalculateEnergyFromKernel(KernelStateBridge<S, T>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.kernel.assigner.KernelAssignerCalculateEnergyFromKernel
- KernelBirth<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
-
Adds a new mark (a "birth") to create a proposal
- KernelBirth() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
- KernelBirthAndKill - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
- KernelBirthAndKill() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- KernelBirthPartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
-
Proposes new marks ONLY if they haven't already been proposed and accepted.
- KernelBirthPartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
- KernelBirthPixelized - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized
-
As an example, this is like sampling WITH replacement.
- KernelBirthPixelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
- KernelBirthPixelized(MarkProposer) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
- KernelCalculateEnergyException - Exception in org.anchoranalysis.mpp.segment.kernel
- KernelCalculateEnergyException(String) - Constructor for exception org.anchoranalysis.mpp.segment.kernel.KernelCalculateEnergyException
- KernelCalculateEnergyException(String, Exception) - Constructor for exception org.anchoranalysis.mpp.segment.kernel.KernelCalculateEnergyException
- KernelCalculationContext - Class in org.anchoranalysis.mpp.segment.kernel
- KernelCalculationContext(MarkFactoryContext, EnergyStack, EnergySchemeWithSharedFeatures, RandomNumberGenerator, ErrorNode) - Constructor for class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
- KernelDeath<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
- KernelDeath() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
- KernelDeath.MarkAnd<S,T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
- KernelDeathPartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
- KernelDeathPartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelDeathPartition
- KernelDeathPixelized - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized
- KernelDeathPixelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelDeathPixelized
- KernelDependent<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel
- KernelDependent() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.KernelDependent
- KernelDescision - Class in org.anchoranalysis.mpp.segment.kernel.proposer
-
A description of the decision made to accept/reject a kernel at a particular time instance (index)
- KernelDescision(KernelWithIdentifier<?>, boolean, boolean, int[], long, int, ProposerFailureDescription) - Constructor for class org.anchoranalysis.mpp.segment.kernel.proposer.KernelDescision
- kernelDescription() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- KernelExchange - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
- KernelExchange() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
- kernelIdentifier() - Method in class org.anchoranalysis.mpp.segment.optimization.step.Reporting
- KernelIndependent<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel
-
A kernel that makes proposals independently of the current state
- KernelIndependent() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.KernelIndependent
- KernelInitialMarksFromPartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
- KernelInitialMarksFromPartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
- KernelInitialMarksProposed - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
- KernelInitialMarksProposed() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
- KernelInitialMarksVoxelized - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
- KernelInitialMarksVoxelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
- KernelInitialMarksVoxelized(MarkCollectionProposer) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
- KernelIterDescriptionSerializerPeriodicReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- KernelIterDescriptionSerializerPeriodicReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.KernelIterDescriptionSerializerPeriodicReporter
- KernelMerge - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
- KernelMerge() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- KernelPosNeg<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel
- KernelPosNeg() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
- KernelProposer<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel.proposer
- KernelProposer() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- KernelProposerOption<T> - Class in org.anchoranalysis.mpp.segment.bean.kernel.proposer
- KernelProposerOption() - Constructor for class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposerOption
- KernelProposerOptionDual<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
- KernelProposerOptionDual() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
- KernelProposerOptionSingle<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
- KernelProposerOptionSingle() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
- KernelProposerOptionSingle(Kernel<T>, double) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
- KernelReplace<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
- KernelReplace() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
- KernelReplacePartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
- KernelReplacePartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelReplacePartition
- KernelSplit - Class in org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
- KernelSplit() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
- kernelStateBridge() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
- kernelStateBridge() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
- kernelStateBridge() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- KernelStateBridge<U,T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
-
Transforms a kernel-to-state and vice versa
- KernelStateBridge() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridge
- KernelStateBridgeIdentity<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
-
No transformation occurs as Kernel and State are the same type
- KernelStateBridgeIdentity() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeIdentity
- KernelStateBridgePixelize<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
-
State derived from the kernel takes the form of
ToPixelized<T> - KernelStateBridgePixelize() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
- KernelStateBridgeTransformer<U,T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
- KernelStateBridgeTransformer() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
- kernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridge
- kernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeIdentity
- kernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
- kernelToState() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
- KernelUpdater<S,T> - Interface in org.anchoranalysis.plugin.mpp.segment.kernel.updater
- KernelUpdaterSimple<S,T> - Class in org.anchoranalysis.plugin.mpp.segment.kernel.updater
- KernelUpdaterSimple(ListUpdatableMarkSetCollection, WeightedKernelList<S>, StateTransformer<Optional<T>, Optional<S>>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.kernel.updater.KernelUpdaterSimple
- KernelWithIdentifier<T> - Class in org.anchoranalysis.mpp.segment.kernel.proposer
- KernelWithIdentifier(Kernel<T>, int) - Constructor for class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
- keys() - Method in interface org.anchoranalysis.core.identifier.provider.NamedProvider
-
Returns a set of keys associated with the provider.
- keys() - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
- keys() - Method in class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
- keys() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
- keys() - Method in class org.anchoranalysis.core.identifier.provider.store.EagerEvaluationStore
- keys() - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
- keys() - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
- keys() - Method in class org.anchoranalysis.image.core.stack.NamedStacks
- keys() - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequence
- keys() - Method in class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
- keys() - Method in class org.anchoranalysis.image.core.stack.wrap.WrapTimeSequenceAsStack
- keySet() - Method in class org.anchoranalysis.core.value.KeyValueParams
- keySet() - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels
- keysEvaluated() - Method in class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
- KeyValueCondition - Class in org.anchoranalysis.plugin.image.bean.params
-
A key and associated value
- KeyValueCondition() - Constructor for class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
- keyValueParams() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- KeyValueParams - Class in org.anchoranalysis.core.value
-
Parameters represented by key/value strings
- KeyValueParams() - Constructor for class org.anchoranalysis.core.value.KeyValueParams
- KeyValueParamsDeserializer<T> - Class in org.anchoranalysis.core.serialize
- KeyValueParamsDeserializer() - Constructor for class org.anchoranalysis.core.serialize.KeyValueParamsDeserializer
- KeyValueParamsForImageCreator - Class in org.anchoranalysis.mpp.feature.energy.scheme
-
Creates KeyValueParams for a particular EnergyStack that is associated with a EnergyScheme
- KeyValueParamsForImageCreator(EnergyScheme, SharedFeatureMulti, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.scheme.KeyValueParamsForImageCreator
- KeyValueParamsGenerator - Class in org.anchoranalysis.io.generator.serialized
- KeyValueParamsGenerator(String) - Constructor for class org.anchoranalysis.io.generator.serialized.KeyValueParamsGenerator
- KeyValueParamsInitParams - Class in org.anchoranalysis.bean.shared.params.keyvalue
- KeyValueParamsProvider - Class in org.anchoranalysis.bean.shared.params.keyvalue
- KeyValueParamsProvider() - Constructor for class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProvider
- KeyValueParamsProviderReference - Class in org.anchoranalysis.bean.shared.params.keyvalue
- KeyValueParamsProviderReference() - Constructor for class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
- kurtosis(Histogram) - Static method in class org.anchoranalysis.math.histogram.HistogramStatistics
- Kurtosis - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- Kurtosis() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Kurtosis
L
- l2norm() - Method in class org.anchoranalysis.spatial.point.Point3d
- labelElements(Channel, List<T>, Optional<Map<Integer, T>>) - Method in class org.anchoranalysis.image.core.object.label.LabelObjects
-
Replaces the contents of the channel so that all element's voxels are labelled with successive unique integer identifiers 1,2,3 etc.
- labelFor(NoSharedState, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
- labelFor(NoSharedState, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
- labelFor(ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
-
Determines a particular group-identifier for an input
- labelFor(ImageCSVLabellerInitParams, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
- labelFor(ImageLabellerStringMapInitParams<T>, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
- labelFor(T, ProvidesStackInput, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabeller
-
Determines a particular group-identifier for an input
- labelForAggregation() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
-
A label to be used when aggregrating this annotation with others, or null if this makes no sense
- LabelHeaders - Class in org.anchoranalysis.feature.io.results
-
Headers in a CSV file for the non-results (i.e.
- LabelHeaders(String[]) - Constructor for class org.anchoranalysis.feature.io.results.LabelHeaders
-
Creates with only non-group headers
- LabelHeaders(String[], String[]) - Constructor for class org.anchoranalysis.feature.io.results.LabelHeaders
- LabelObjects<T> - Class in org.anchoranalysis.image.core.object.label
-
Writes a unique ID (successive integer IDs) for each elements's voxels into a channel, and 0 for background.
- LabelObjects(Function<T, ObjectMask>, BiFunction<T, ReadableTuple3i, T>) - Constructor for class org.anchoranalysis.image.core.object.label.LabelObjects
- LabelObjects(Optional<UnaryOperator<T>>, Optional<Consumer<OverlappingObject<T>>>, Function<T, ObjectMask>, BiFunction<T, ReadableTuple3i, T>) - Constructor for class org.anchoranalysis.image.core.object.label.LabelObjects
- labels() - Method in class org.anchoranalysis.image.experiment.label.FileLabelMap
- LanguageUtilities - Class in org.anchoranalysis.core.value
- lastConnectedTo(ContourList) - Method in class org.anchoranalysis.plugin.points.contour.ContourList
- LastDirectories - Class in org.anchoranalysis.plugin.io.bean.descriptivename
-
Derives a name by taking the filename together with optionally several subdirectories names.
- LastDirectories() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
- LastDirectories(int) - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
-
Creates for a particular number of subdirectories.
- LastDirectoryAsPrefix - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
-
Looks for the last directory-name, and removes it in favour of using it as a prefix on a filename
- LastDirectoryAsPrefix() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
- lastIndex(String) - Method in class org.anchoranalysis.io.generator.sequence.SequenceMemory
- lastIndexOf(Object) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- lastIndexOf(Object) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- Launch - Class in org.anchoranalysis.launcher
-
A command-line interface used for launching experiments
- LauncherConfig - Class in org.anchoranalysis.launcher.config
- LauncherConfig() - Constructor for class org.anchoranalysis.launcher.config.LauncherConfig
- LaunchInteractiveBrowser - Class in org.anchoranalysis.browser.launcher
-
Command-line application for launching the anchor GUI application, otherwise known as interactive-browser.
- LazyEvaluationStore<T> - Class in org.anchoranalysis.core.identifier.provider.store
-
Items are evaluated only when they are first needed.
- LazyEvaluationStore(String) - Constructor for class org.anchoranalysis.core.identifier.provider.store.LazyEvaluationStore
- leftSize() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- LegacyOutputEnabled - Class in org.anchoranalysis.plugin.mpp.experiment.bean.output
-
Deprecated.Prefer another sub-class of
OutputEnabledRules. - LegacyOutputEnabled() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
-
Deprecated.
- length() - Method in class org.anchoranalysis.feature.results.ResultsVector
- length() - Method in class org.anchoranalysis.spatial.point.Vector3d
- LessThan - Class in org.anchoranalysis.math.relation
- LessThan() - Constructor for class org.anchoranalysis.math.relation.LessThan
- LessThanBean - Class in org.anchoranalysis.bean.shared.relation
- LessThanBean() - Constructor for class org.anchoranalysis.bean.shared.relation.LessThanBean
- LessThanEqualTo - Class in org.anchoranalysis.math.relation
- LessThanEqualTo() - Constructor for class org.anchoranalysis.math.relation.LessThanEqualTo
- LessThanEqualToBean - Class in org.anchoranalysis.bean.shared.relation
- LessThanEqualToBean() - Constructor for class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
- LevelFromHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
-
Calculates a level (a threshold-value) from a histogram.
- LevelFromHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
- LevelPerObjectBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object
-
Creates a channel with a level calculated for each object variously
- LevelPerObjectBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
- LevelPerObjectIndependently - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object
-
Creates a channel with different threshold-levels for each object, calculating the level only from the histogram of the particular object.
- LevelPerObjectIndependently() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
- LevelPerObjectNeighbors - Class in org.anchoranalysis.plugin.image.bean.channel.provider.object
-
Calculates a threshold-level for each object collectively based on other objects
- LevelPerObjectNeighbors() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
- LevelResult - Class in org.anchoranalysis.plugin.image.intensity.level
- LevelResult(int, ObjectMask, Histogram) - Constructor for class org.anchoranalysis.plugin.image.intensity.level.LevelResult
- LevelResultCollection - Class in org.anchoranalysis.plugin.image.intensity.level
- LevelResultCollection() - Constructor for class org.anchoranalysis.plugin.image.intensity.level.LevelResultCollection
- LevelResultCollectionFactory - Class in org.anchoranalysis.plugin.image.intensity.level
- Limit<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Limits the number of input-objects to a certain hard-maximum
- Limit - Class in org.anchoranalysis.plugin.io.bean.provider.file
- Limit() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Limit
- Limit() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.Limit
- LimitWithDirectory - Class in org.anchoranalysis.plugin.io.bean.provider.file
- LimitWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.LimitWithDirectory
- LinearLeastSquaresEllipseFitter - Class in org.anchoranalysis.plugin.points.bean.fitter
-
Fits a set of points to an ellipse using a linear least squares method.
- LinearLeastSquaresEllipseFitter() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
- LinearLeastSquaresEllipsoidFitter - Class in org.anchoranalysis.plugin.points.bean.fitter
-
Fits an ellipsoid to points using a linear least squares approach
- LinearLeastSquaresEllipsoidFitter() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
- LinearLeastSquaresViaNormalEquationBase - Class in org.anchoranalysis.plugin.points.bean.fitter
- LinearLeastSquaresViaNormalEquationBase() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
- LineBoundCalculator - Class in org.anchoranalysis.plugin.mpp.bean.bound
- LineBoundCalculator() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
- LinePlot<T extends IndexGetter> - Class in org.anchoranalysis.plot.index
-
A line graph with 1 or more series, with an index on the x-axis.
- LinePlot(String, String[], LinePlot.YValGetter<T>) - Constructor for class org.anchoranalysis.plot.index.LinePlot
- LinePlot.YValGetter<T> - Interface in org.anchoranalysis.plot.index
- LineSegment - Class in org.anchoranalysis.mpp.mark.points
- LineSegment() - Constructor for class org.anchoranalysis.mpp.mark.points.LineSegment
- LineSegment(Point3i, Point3i) - Constructor for class org.anchoranalysis.mpp.mark.points.LineSegment
- list() - Method in class org.anchoranalysis.bean.StringList
- list() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
- list() - Method in class org.anchoranalysis.spatial.box.BoundedList
-
The collection of element with bounding-boxes.
- ListBeanFactory<T> - Class in org.anchoranalysis.bean.xml.factory
-
Factory for creating a java.util.List of Beans
- ListBeanFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.ListBeanFactory
- ListBeanFactory(CreateFromList<T>) - Constructor for class org.anchoranalysis.bean.xml.factory.ListBeanFactory
- ListBoundCalculator - Class in org.anchoranalysis.plugin.mpp.bean.bound
- ListBoundCalculator() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.ListBoundCalculator
- listFeatures() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
- listFeaturesSubset(int, int) - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
- listFrom2i(Mask) - Static method in class org.anchoranalysis.image.core.points.PointsFromMask
- listFrom2i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
-
A list of two-dimensional integer points from the entire object-mask
- listFrom3d(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
-
A list of points from the entire object-mask
- listFrom3i(Mask) - Static method in class org.anchoranalysis.image.core.points.PointsFromMask
- listFrom3i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
-
A list of three-dimensional integer points from the entire object-mask
- listFromAllOutlines2i(ObjectCollection) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
-
A list of points as three-dimensional integers from the outline of all objects in a collection
- listFromOutline2i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
-
A list of points as three-dimensional integers from the outline of an object-mask
- listFromOutline3i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
-
A list of points as three-dimensional integers from the outline of an object-mask
- listFromSlicesInsideBox3i(Mask, BoundingBox, int, int) - Static method in class org.anchoranalysis.image.core.points.PointsFromMask
- listIterator() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- listIterator(int) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- listOfBeans(String, HierarchicalConfiguration, Object) - Static method in class org.anchoranalysis.bean.xml.factory.HelperListUtilities
-
A list of instantiated bean objects from an XML configuration
- listProbMap() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- ListSequence<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
-
Populates a FeatureListElem with references to other features formed by one or two sequences of integers, so that all the features of the following pattern are contained in the list.
- ListSequence() - Constructor for class org.anchoranalysis.feature.bean.list.ListSequence
- ListUpdatableMarkSetCollection - Class in org.anchoranalysis.mpp.feature.mark
- ListUpdatableMarkSetCollection() - Constructor for class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- ListWithThumbnails<T,S> - Class in org.anchoranalysis.plugin.image.feature.object
-
A list of items with an associated thumbnail-batch
- ListWithThumbnails(List<T>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
- ListWithThumbnails(List<T>, ThumbnailBatch<S>) - Constructor for class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
- loadBean(Path) - Static method in class org.anchoranalysis.bean.xml.BeanXmlLoader
-
Creates a bean by loading an XML description from the filesystem
- loadBean(Path, String) - Static method in class org.anchoranalysis.bean.xml.BeanXmlLoader
-
Creates a bean by loading an XML description from the filesystem
- loadBeanAssociatedXml(Path, String) - Static method in class org.anchoranalysis.bean.xml.BeanXmlLoader
-
Creates a bean by loading an XML description from the filesystem
- loadBeanLocalized(Path, String) - Static method in class org.anchoranalysis.bean.xml.BeanXmlLoader
-
Creates a bean by loading an XML description from the filesystem
- localise(Path) - Method in class org.anchoranalysis.bean.AnchorBean
-
Called once after the bean is created, localising the bean to a path on the filesystem.
- localise(Path) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- localise(Path) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- LocalisedBeanException - Exception in org.anchoranalysis.bean.xml.error
-
Combines many exceptions into a single exception, searching for a Cause and creating message string, incorporating the other strings
- LocalisedBeanException(String, Throwable) - Constructor for exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
- LocalSlices - Class in org.anchoranalysis.image.voxel.kernel
- LocalSlices(int, int, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.kernel.LocalSlices
- log(String) - Method in interface org.anchoranalysis.core.log.MessageLogger
- log(String) - Method in class org.anchoranalysis.core.log.NullMessageLogger
- log(String) - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
- log(String) - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
- log(String) - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
- log(String) - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
- log(String) - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
- Log4JReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- Log4JReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
- logDescription() - Method in class org.anchoranalysis.plugin.image.object.merge.GraphLogger
- logEnd(JobDescription, JobState, boolean) - Method in class org.anchoranalysis.experiment.task.processor.JobStartStopLogger
-
Performs logging for when a job ends.
- logFormatted(String, Object...) - Method in interface org.anchoranalysis.core.log.MessageLogger
- logFormatted(String, Object...) - Method in class org.anchoranalysis.core.log.NullMessageLogger
- logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
- logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
- logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
- logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
- logFormatted(String, Object...) - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
- Logger - Class in org.anchoranalysis.core.log
-
A logging-mechanism for both messages and errors.
- Logger(MessageLogger) - Constructor for class org.anchoranalysis.core.log.Logger
-
Constructs with an error-reporter that writes into the message logger.
- Logger(MessageLogger, ErrorReporter) - Constructor for class org.anchoranalysis.core.log.Logger
- loggerForMonitor(ParametersExperiment) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
- LoggingDestination - Class in org.anchoranalysis.experiment.bean.log
-
The destination(s) to which log-messages are sent.
- LoggingDestination() - Constructor for class org.anchoranalysis.experiment.bean.log.LoggingDestination
- LoggingFixture - Class in org.anchoranalysis.test
-
Fixtures to create loggers that don't output anything
- logGraphDescription() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
- logMemoryUsage(String, MessageLogger) - Static method in class org.anchoranalysis.core.system.MemoryUtilities
- logStart(JobDescription) - Method in class org.anchoranalysis.experiment.task.processor.JobStartStopLogger
-
Performs logging for when a job starts.
- LogUtilities - Class in org.anchoranalysis.core.log
- LongestExtent - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
- LongestExtent() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
- LongestExtentWithin - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
- LongestExtentWithin() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
- LoopablePoints - Class in org.anchoranalysis.image.core.outline.traverser.visited
-
A set of points that can be looped, so as to form a path that ends with the same point that it begins with....
- LoopablePoints(List<Point3i>, Point3i) - Constructor for class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
- loopPointsLeft() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
- loopPointsRight() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
- lowerCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
- lowerCountExistsThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
- lowerCountExistsThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.predicate.VoxelsPredicate
-
Whether the count is less than a particular threshold.
- LRUCache<K,V> - Class in org.anchoranalysis.core.cache
-
A cache that discards items that haven't being used recently or frequently (as per Guava's size-based eviction's defaults)
- LRUCache(int, CheckedFunction<K, V, E>) - Constructor for class org.anchoranalysis.core.cache.LRUCache
-
Constructor
M
- main(String[]) - Static method in class org.anchoranalysis.browser.launcher.LaunchInteractiveBrowser
-
Entry point for command-line application
- main(String[]) - Static method in class org.anchoranalysis.launcher.Launch
-
Entry point for command-line application
- makeOutputPath(String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
-
Creates a full absolute path that completes the part of the path present in the outputter with an additional suffix.
- makeOutputPath(String, String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
-
Like
OutputterChecked.makeOutputPath(String)but additionally adds an extension. - makePathAbsolute(String) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
- makePathAbsolute(String) - Method in interface org.anchoranalysis.io.output.path.prefixer.PathCreator
-
Generates a full path, given the final part (suffix) of a path.
- makePathRelative(Path) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
- makePathRelative(Path) - Method in interface org.anchoranalysis.io.output.path.prefixer.PathCreator
-
Extracts a relative-file path, given the final part (suffix) of a path.
- makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
- makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
- makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- makeProposal(Optional<VoxelizedMarksWithEnergy>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
- makeProposal(Optional<MarkCollection>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
- makeProposal(Optional<MarksFromPartition>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelReplacePartition
- makeProposal(Optional<MarksFromPartition>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
- makeProposal(Optional<T>, KernelCalculationContext) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
-
Calculates the Energy for a proposal
- makeProposal(Optional<T>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
- makeProposal(Optional<T>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
- makeProposal(Optional<T>, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
- makeRGBStack(Stack) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertToMat
- makeSureConfigured() - Method in class org.anchoranalysis.io.bioformats.ConfigureBioformatsLogging
-
Makes sure logging is configured
- Manifest - Class in org.anchoranalysis.io.manifest
-
A manifest for a particular experiment, that may refer to the outputs from particular jobs, each with their own manifest.
- Manifest() - Constructor for class org.anchoranalysis.io.manifest.Manifest
- MANIFEST_FUNCTION - Static variable in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
- MANIFEST_FUNCTION - Static variable in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
- manifestCouplingDefinition(InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
- ManifestCouplingDefinition - Class in org.anchoranalysis.plugin.io.manifest
- ManifestCouplingDefinition() - Constructor for class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
- ManifestDescription - Class in org.anchoranalysis.io.manifest
-
A description of an entry (e.g.
- ManifestDescription(String, String) - Constructor for class org.anchoranalysis.io.manifest.ManifestDescription
- ManifestDeserializer - Interface in org.anchoranalysis.io.manifest.deserializer
- ManifestDirectoryDescription - Class in org.anchoranalysis.io.manifest
-
A description of an directory in the manifest.
- ManifestDirectoryDescription(String, String, SequenceType<?>) - Constructor for class org.anchoranalysis.io.manifest.ManifestDirectoryDescription
- ManifestDirectoryDescription(Optional<ManifestDescription>, SequenceType<?>) - Constructor for class org.anchoranalysis.io.manifest.ManifestDirectoryDescription
- ManifestGenerator - Class in org.anchoranalysis.io.generator.combined
- ManifestGenerator() - Constructor for class org.anchoranalysis.io.generator.combined.ManifestGenerator
- map(Function<T, S>) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
-
Maps the existing object to another object, while retaining an identical confidence score.
- map(UnaryOperator<ObjectMask>) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
-
Maps the underlying object-mask to another object-mask, reusing the same properties object.
- map(Optional<S>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
-
Like
Optional.map(java.util.function.Function<? super T, ? extends U>)but tolerates an exception in the mapping function, which is immediately thrown. - map(Stream<S>, Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
-
Performs a
Stream.map(java.util.function.Function<? super T, ? extends R>)but accepts a function that can throw a checked-exception - map(CheckedFunction<Feature<T>, Feature<S>, E>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
-
Creates a new feature-list where each feature is the result of applying a map-function to an existing feature
- map(CheckedFunction<ObjectMask, ObjectMask, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Creates a new
ObjectCollectionafter mapping each item to another. - mapBoth(Optional<U>, Optional<V>, CheckedBiFunction<U, V, T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
-
Mapping only occurs if both Optionals are non-empty (equivalent to a logical AND on the optionals)
- mapBoundingBoxChangeExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Applies a function to map the bounding-box to a new-value (whose extent is expected to change in value)
- mapBoundingBoxChangeExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Creates a new
ObjectCollectionafter mapping the bounding-box on each object (while maybe changing the extent). - mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Applies a function to map the bounding-box to a new-value (whose extent should be unchanged in value)
- mapBoundingBoxPreserveExtent(UnaryOperator<BoundingBox>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Creates a new
ObjectCollectionafter mapping the bounding-box on each object (whose extent should remain unchanged). - mapBoundingBoxPreserveExtent(BoundingBox) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
Applies a function to map the bounding-box to a new-value (whose extent should be unchanged in value)
- mapCalculator(UnaryOperator<FeatureCalculatorMulti<T>>) - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
- mapChannel(CheckedUnaryOperator<Channel, OperationFailedException>) - Method in class org.anchoranalysis.image.core.stack.Stack
-
Produces a new stack with a particular mapping applied to each channel.
- mapChannelIfSupported(int, BiFunction<Channel, ChannelConverterAttached<Channel, UnsignedByteBuffer>, T>, Function<Channel, T>) - Method in class org.anchoranalysis.image.core.stack.ChannelMapper
- mapChannelWithIndex(CheckedBiFunction<Channel, Integer, Channel, OperationFailedException>) - Method in class org.anchoranalysis.image.core.stack.Stack
-
Produces a new stack with a particular mapping applied to each channel (with an index of the channel also available)
- MapCreate<K,V> - Class in org.anchoranalysis.core.identifier.name
-
A tree map that creates a new item, if it doesn't already exist, after a GET operation
- MapCreate(Supplier<V>) - Constructor for class org.anchoranalysis.core.identifier.name.MapCreate
- MapCreate(Supplier<V>, Comparator<K>) - Constructor for class org.anchoranalysis.core.identifier.name.MapCreate
- mapFrom(Iterable<S>, CheckedFunction<S, Feature<T>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
- mapFrom(Iterable<T>, CheckedFunction<T, ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection by mapping an
IterabletoObjectMask - mapFromFiltered(Iterable<S>, Predicate<S>, CheckedFunction<S, Feature<T>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
-
Creates a new feature-list by filtering an iterable and then mapping it to a feature
- mapFromOptional(Iterable<T>, CheckedFunction<T, Optional<ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
- mapFromOptional(Iterator<T>, CheckedFunction<T, Optional<ObjectMask>, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
- mapFromRange(int, int, Class<? extends Exception>, CheckedIntFunction<ObjectMask, E>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection by mapping integers (from a range) each to a
ObjectMask - mapFromRange(int, int, IntFunction<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
-
Creates a new feature-list by mapping integers (from a range) each to a feature
- mapFromRange(int, int, IntFunction<ObjectMask>) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection by mapping integers (from a range) each to a
ObjectMask - mapFromRangeOptional(int, int, Class<? extends Exception>, CheckedIntFunction<Optional<Feature<T>>, E>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
-
Creates a new feature-list by mapping integers (from a range) each to an optional feature
- MapGroupToRow - Class in org.anchoranalysis.plugin.mpp.experiment.objects.csv
-
Maps Group (String) to a CSVRow
- MapGroupToRow() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.objects.csv.MapGroupToRow
- mapIntStream(IntStream, Class<? extends Exception>, CheckedIntFunction<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
-
Creates a new feature-list by mapping integers (from a range) each to an optional feature accepting a checked-exception
- mapList(List<S>, ProgressReporter, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalProgress
-
Maps a list to new list, updating a progress-reporter for every element
- mapListOptional(List<S>, ProgressReporter, CheckedFunction<S, Optional<T>, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalProgress
-
Maps a list to a new list, including only certain items, updating a progress-reporter for every element
- mapRangeToList(int, int, IntFunction<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Creates a list of elements, where each element corresponds to an index in a range.
- mapToInt(Stream<S>, Class<? extends Exception>, CheckedToIntFunction<S, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
-
Performs a
Stream.mapToInt(java.util.function.ToIntFunction<? super T>)but accepts a function that can throw a checked-exception. - mapToList(Collection<S>, Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Like
FunctionalList.mapToList(Object[], Function)but tolerates exceptions in the mapping function. - mapToList(Collection<S>, Function<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Maps a collection to a list with each element derived from a corresponding element in the original collection.
- mapToList(Stream<S>, Function<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Maps a stream to a list with each element derived from a corresponding element in the original collection.
- mapToList(CheckedFunction<ObjectMask, T, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Creates a new
Listafter mapping each item to another type. - mapToList(S[], Class<? extends Exception>, CheckedFunction<S, T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Like
FunctionalList.mapToList(Object[], Function)but tolerates exceptions in the mapping function. - mapToList(S[], Function<S, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Maps an array to a list with each element derived from a corresponding element in the original array.
- mapToListOptional(Collection<S>, Function<S, Optional<T>>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Maps a collection to a list with each element in the original collection maybe producing an element in the output
- mapToListOptional(CheckedFunction<ObjectMask, Optional<T>, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Creates a new
Listafter mapping each item to another (optional) type - mapToListWithIndex(List<S>, BiFunction<S, Integer, T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Maps a collection to a list with each element derived from a corresponding element in the original collection - and also letting the map function use an index.
- mapToObj(IntStream, Class<? extends Exception>, CheckedIntFunction<T, E>) - Static method in class org.anchoranalysis.core.functional.CheckedStream
-
Performs a
IntStream.mapToObj(java.util.function.IntFunction<? extends U>)but accepts a function that can throw a checked-exception. - mapToSortedSet(CheckedFunction<ObjectMask, T, E>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Creates a new
SortedSetafter mapping each item to another type. - Mark - Class in org.anchoranalysis.mpp.mark
- Mark() - Constructor for class org.anchoranalysis.mpp.mark.Mark
- Mark(Mark) - Constructor for class org.anchoranalysis.mpp.mark.Mark
-
Copy constructor
- MarkAnd(S, T) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
- MarkAnnotationDeleter - Class in org.anchoranalysis.annotation.io.mark
- MarkAnnotationDeleter() - Constructor for class org.anchoranalysis.annotation.io.mark.MarkAnnotationDeleter
- MarkAnnotationReader<T> - Class in org.anchoranalysis.annotation.io.mark
-
Reads a
DualMarksAnnotationfrom a path on the filesystem. - MarkAnnotationReader(boolean) - Constructor for class org.anchoranalysis.annotation.io.mark.MarkAnnotationReader
- MarkAnnotationWriter<T> - Class in org.anchoranalysis.annotation.io.mark
- MarkAnnotationWriter() - Constructor for class org.anchoranalysis.annotation.io.mark.MarkAnnotationWriter
- markAsCompleted(boolean) - Method in class org.anchoranalysis.experiment.task.processor.JobState
- markAsExecuting() - Method in class org.anchoranalysis.experiment.task.processor.JobState
- markAsTemporary(int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
- MarkBounds - Class in org.anchoranalysis.mpp.bean.bound
- MarkBounds() - Constructor for class org.anchoranalysis.mpp.bean.bound.MarkBounds
- MarkBoundsDefine - Class in org.anchoranalysis.plugin.mpp.bean.bound
- MarkBoundsDefine() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
- MarkBoundsDefine(MarkBounds) - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
- MarkBoundsProvider - Class in org.anchoranalysis.mpp.bean.provider
- MarkBoundsProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MarkBoundsProvider
- MarkBoundsReference - Class in org.anchoranalysis.plugin.mpp.bean.bound
- MarkBoundsReference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsReference
- MarkCollection - Class in org.anchoranalysis.mpp.mark
-
A collection of marks, termed a configuration in marked-point-processes academic literature.
- MarkCollection() - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
- MarkCollection(List<Mark>) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
- MarkCollection(Stream<Mark>) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
- MarkCollection(Mark) - Constructor for class org.anchoranalysis.mpp.mark.MarkCollection
- MarkCollectionDeserializer - Class in org.anchoranalysis.mpp.io.marks
- MarkCollectionDeserializer() - Constructor for class org.anchoranalysis.mpp.io.marks.MarkCollectionDeserializer
- MarkCollectionProposer - Class in org.anchoranalysis.mpp.bean.proposer
-
Proposes an entire collection (confguration) of marks
- MarkCollectionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkCollectionProposer
- MarkCollectionProvider - Class in org.anchoranalysis.mpp.bean.provider
-
Provides a collection of marks
- MarkCollectionProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MarkCollectionProvider
- MarkConicFactory - Class in org.anchoranalysis.mpp.mark.conic
- MarkDistance - Class in org.anchoranalysis.mpp.bean.mark
- MarkDistance() - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkDistance
- MarkDistanceAbstractPosition - Class in org.anchoranalysis.plugin.mpp.bean.distance
- MarkDistanceAbstractPosition() - Constructor for class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceAbstractPosition
- MarkDistanceRadii - Class in org.anchoranalysis.plugin.mpp.bean.distance
- MarkDistanceRadii() - Constructor for class org.anchoranalysis.plugin.mpp.bean.distance.MarkDistanceRadii
- MarkEllipseCircumEstimate - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
-
Estimates the circumference of an ellipse based upon finding the area of the shell, and dividing // by the ShellRad
- MarkEllipseCircumEstimate() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.MarkEllipseCircumEstimate
- MarkEllipseFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
- MarkEllipseFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
- MarkEllipseSimple - Class in org.anchoranalysis.plugin.mpp.bean.proposer.split
- MarkEllipseSimple() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
- MarkEllipsoidFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
- MarkEllipsoidFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
- MarkEvaluator - Class in org.anchoranalysis.mpp.feature.bean.mark
- MarkEvaluator() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
- MarkFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
- MarkFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkFactory
- markFactoryContext() - Method in class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
- MarkFactoryContext - Class in org.anchoranalysis.mpp.segment.kernel
- MarkFactoryContext(MarkWithIdentifierFactory) - Constructor for class org.anchoranalysis.mpp.segment.kernel.MarkFactoryContext
- MarkFromCollectionProposer - Class in org.anchoranalysis.mpp.bean.proposer
- MarkFromCollectionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkFromCollectionProposer
- MarkFromCollectionProposerUnary - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
- MarkFromCollectionProposerUnary() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
- MarkMergeProposer - Class in org.anchoranalysis.mpp.bean.proposer
- MarkMergeProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
- MarkMergeProposerReference - Class in org.anchoranalysis.plugin.mpp.bean.proposer.merge
- MarkMergeProposerReference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
- markNoProposal(ProposerFailureDescription) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- MarkPairCollection - Class in org.anchoranalysis.mpp.feature.mark
-
A pair collection where the underlying type is a simple
IdentifiablePair - MarkPairCollection() - Constructor for class org.anchoranalysis.mpp.feature.mark.MarkPairCollection
- MarkPointListFactory - Class in org.anchoranalysis.mpp.bean.mark.factory
- MarkPointListFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.factory.MarkPointListFactory
- MarkProposer - Class in org.anchoranalysis.mpp.bean.proposer
- MarkProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkProposer
- MarkProposerFromList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
- MarkProposerFromList() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
- MarkProposerReference - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
- MarkProposerReference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
- MarkProposerStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
-
Annotates each image with a mark
- MarkProposerStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
- MarkProposerUnary - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
- MarkProposerUnary() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
- MarkProviderPointsFitterFromConvexHull - Class in org.anchoranalysis.plugin.points.bean.mark.provider.single
- MarkProviderPointsFitterFromConvexHull() - Constructor for class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- MarkRegion - Class in org.anchoranalysis.mpp.bean.mark
- MarkRegion() - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkRegion
- marks() - Method in interface org.anchoranalysis.annotation.mark.AnnotationWithMarks
-
The marks associated with the annotation
- marks() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
- marks() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- MARKS - Static variable in class org.anchoranalysis.mpp.segment.define.OutputterDirectories
-
Where collections of marks are typically placed in a define-experiment output
- MarksAsUniqueValueGenerator - Class in org.anchoranalysis.mpp.io.marks.generator
- MarksAsUniqueValueGenerator(Dimensions, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksAsUniqueValueGenerator
- marksAt(Point3d, RegionMap, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- MarksComparer - Class in org.anchoranalysis.plugin.annotation.bean.comparer
- MarksComparer() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.MarksComparer
- marksDeriver() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
- MarksFlattenedGenerator - Class in org.anchoranalysis.mpp.io.marks.generator
- MarksFlattenedGenerator(DrawObject, IdentifierGetter<Overlay>, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksFlattenedGenerator
- MarksFromEnergyHelper - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
- marksFromMemo(MemoCollection) - Static method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MarksFromEnergyHelper
- marksFromOverlays(ColoredOverlayCollection) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory
- marksFromOverlays(OverlayCollection) - Static method in class org.anchoranalysis.mpp.overlay.OverlayCollectionMarkFactory
- MarksFromPartition - Class in org.anchoranalysis.plugin.mpp.segment.optimization
-
A subset of a marks (as extracted during a partition)
- MarksFromPartition(MarkCollection, PartitionedMarks) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.MarksFromPartition
- MarksGenerator - Class in org.anchoranalysis.mpp.io.marks.generator
- MarksGenerator(DrawObject, IdentifierGetter<Overlay>) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksGenerator
- MarksGenerator(DrawObject, IdentifierGetter<Overlay>, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksGenerator
- MarksGeneratorBase - Class in org.anchoranalysis.mpp.io.marks.generator
- MarksGeneratorBase(DrawOverlay, IdentifierGetter<Overlay>, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
- marksNew() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
- MarkSplitProposer - Class in org.anchoranalysis.mpp.bean.proposer
- MarkSplitProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.MarkSplitProposer
- MarkSplitProposerReference - Class in org.anchoranalysis.plugin.mpp.bean.proposer.split
- MarkSplitProposerReference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
- MarksWithDisplayStack - Class in org.anchoranalysis.mpp.io.marks
- MarksWithDisplayStack(MarkCollection, DisplayStack) - Constructor for class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
- MarksWithEnergyBreakdown - Class in org.anchoranalysis.mpp.feature.energy.marks
-
Marks with both the total energy and a breakdown by clique
- MarksWithEnergyBreakdown(MarksWithTotalEnergy) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- MarksWithEnergyBreakdown(MarksWithTotalEnergy, EnergySavedInd, EnergySavedPairs, EnergySavedAll) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- MarksWithTotalEnergy - Class in org.anchoranalysis.mpp.feature.energy.marks
-
A collection of marks with an associated (total) energy.
- MarksWithTotalEnergy(MarkCollection, EnergySchemeWithSharedFeatures) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
- MarkWithIdentifierFactory - Class in org.anchoranalysis.mpp.bean.mark
- MarkWithIdentifierFactory() - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
- MarkWithIdentifierFactory(MarkFactory) - Constructor for class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
- MarkWithPosition - Class in org.anchoranalysis.mpp.mark
- MarkWithPosition() - Constructor for class org.anchoranalysis.mpp.mark.MarkWithPosition
- MarkWithPosition(MarkWithPosition) - Constructor for class org.anchoranalysis.mpp.mark.MarkWithPosition
- MarkWithPositionAndSingleRadius - Class in org.anchoranalysis.mpp.mark.conic
-
Base-class for a conic that has a single radius (circle, sphere etc.)
- MarkWithPositionAndSingleRadius() - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- MarkWithPositionAndSingleRadius(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
-
Constructor with a bound on the radius
- MarkWithPositionAndSingleRadius(MarkWithPositionAndSingleRadius) - Constructor for class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
-
Copy constructor
- mask(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
- Mask - Class in org.anchoranalysis.image.core.mask
-
A channel that is restricted to two values (ON and OFF) so as to act like a mask.
- Mask(Channel) - Constructor for class org.anchoranalysis.image.core.mask.Mask
-
Creates a mask from an existing channel using default values for OFF (0) and ON (255)
- Mask(Channel, BinaryValues) - Constructor for class org.anchoranalysis.image.core.mask.Mask
-
Creates a mask from an existing channel
- Mask(Dimensions, BinaryValues) - Constructor for class org.anchoranalysis.image.core.mask.Mask
-
Creates a new empty mask of particular dimensions and with particular binaryvalues
- Mask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.core.mask.Mask
-
Creates a mask from an existing binary-voxels using default image resolution
- Mask(BinaryVoxels<UnsignedByteBuffer>, Optional<Resolution>) - Constructor for class org.anchoranalysis.image.core.mask.Mask
-
Creates a mask from an existing binary-voxels and a specific image resolution.
- MaskAnd - Class in org.anchoranalysis.image.core.mask.combine
- MaskAsSingleObject<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
-
Calculate a feature, treating a mask as a single-object on the energy-stack
- MaskAsSingleObject() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
- MaskComparer - Class in org.anchoranalysis.plugin.annotation.bean.comparer
- MaskComparer() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
- MaskFactory - Class in org.anchoranalysis.image.core.mask
-
Helper routines to create new instances of
Mask - MaskFromObjects - Class in org.anchoranalysis.image.core.mask
-
Creates a mask from one or more objects.
- MaskIfHighLow - Class in org.anchoranalysis.image.core.mask.combine
- MaskIntersectionAssigner - Class in org.anchoranalysis.plugin.annotation.bean.comparison.assigner
- MaskIntersectionAssigner() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
- MaskInverter - Class in org.anchoranalysis.image.core.mask
-
Inverts masks and objects
- MaskOr - Class in org.anchoranalysis.image.core.mask.combine
- MaskProvider - Class in org.anchoranalysis.image.bean.provider
- MaskProvider() - Constructor for class org.anchoranalysis.image.bean.provider.MaskProvider
- MaskProviderUnary - Class in org.anchoranalysis.image.bean.provider
- MaskProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.MaskProviderUnary
- masks() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- maskScaledXY(Dimensions, RegionMembershipWithFlags, BinaryValuesByte, double) - Method in class org.anchoranalysis.mpp.mark.Mark
- MaskXor - Class in org.anchoranalysis.image.core.mask.combine
- match(int, int) - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
-
Helper method to record a matching between worker w and job j.
- match(String) - Method in class org.anchoranalysis.bean.shared.regex.RegEx
-
Returns an array of string components it matches successfully, or empty() if it cannot match
- match(String) - Method in class org.anchoranalysis.bean.shared.regex.RegExList
- match(String) - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
- match(VoxelDataType) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
- match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
- match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
- match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
- match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
-
A predicate condition for an object to be kept in the collection
- match(ObjectMask, Optional<Dimensions>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
- match(ObjectMask, Optional<Dimensions>, RelationToValue) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
- match(ObjectMask, Optional<Dimensions>, RelationToValue) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
- match(ObjectMask, Optional<Dimensions>, RelationToValue) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
- match(ObjectMask, Optional<Dimensions>, RelationToValue) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
- Match - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
- Match() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
- matchDirectories() - Method in class org.anchoranalysis.io.manifest.finder.FinderSingleDirectory
- MatchedAppendCsv - Class in org.anchoranalysis.plugin.quick.bean.input.filepathappend
-
An append CSV and corresponding match value
- MatchedAppendCsv() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
- MatchedObject - Class in org.anchoranalysis.image.core.object
-
An object with associated matches.
- MatchedObject(ObjectMask, ObjectCollection) - Constructor for class org.anchoranalysis.image.core.object.MatchedObject
- MatcherIntersectionHelper - Class in org.anchoranalysis.plugin.image.bean.object.match
- matchingFilesForDirectory(Path, InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
- matchingFilesForDirectory(Path, InputManagerParams) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.FileSetFromStringSet
- matchIntersectingObjects(ObjectCollection, ObjectCollection) - Static method in class org.anchoranalysis.plugin.image.bean.object.match.MatcherIntersectionHelper
- max() - Method in class org.anchoranalysis.plugin.annotation.comparison.RangeSum
- max(boolean) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- max(double) - Method in class org.anchoranalysis.spatial.point.Point3d
-
Element-wise maximum between this point and a scalar
- max(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
-
Element-wise maximum between this point and a scalar
- max(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i
-
Element-wise maximum between this point and another
- max(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Point3d
-
Element-wise maximum between this point and another
- Max - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- Max() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Max
- MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
- MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType
- MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType
- MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedIntVoxelType
- MAX_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType
- MAX_VALUE - Static variable in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
- MAX_VALUE_INT - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedByteVoxelType
- MAX_VALUE_INT - Static variable in class org.anchoranalysis.image.voxel.datatype.UnsignedShortVoxelType
- maxAsInt(ToIntFunction<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Finds the maximum value of a function applied to each object in the collection.
- MaxDensityKernel3 - Class in org.anchoranalysis.image.voxel.kernel.density
-
Erosion with a 3x3 or 3x3x3 kernel
- MaxDensityKernel3(BinaryValuesByte, boolean, boolean, int) - Constructor for class org.anchoranalysis.image.voxel.kernel.density.MaxDensityKernel3
- maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
- maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
- maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
- maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
- maxDistanceFromRootPoint(Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
- maxDistanceToClosestPoint(ContiguousVoxelPath, Point3i) - Static method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceToContiguousPath
-
The maximum-distance of a point to the closest point on the path
- maxDistanceToHeadTail(ContiguousVoxelPath, Point3i) - Static method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceToContiguousPath
- MaxFeatureIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
-
1.
- MaxFeatureIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MaxFeatureIntersectingObjects
- Maximum - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
The maximum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
- Maximum<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
- Maximum() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Maximum
- Maximum() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.Maximum
- MAXIMUM - org.anchoranalysis.core.index.bounded.BoundChangeEvent.BoundType
- MaximumIntensityProjection - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
- MaximumIntensityProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MaximumIntensityProjection
- MaximumNumberContourVoxelsOnSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.slice
-
Maximum number of voxels on any slice's contour (edge voxels) across all slices.
- MaximumNumberContourVoxelsOnSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberContourVoxelsOnSlice
- MaximumNumberVoxelsOnSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.slice
-
Maximum number of voxels in the object-mask across all slices.
- MaximumNumberVoxelsOnSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.slice.MaximumNumberVoxelsOnSlice
- MaxIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel
- MaxIntensity() - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.MaxIntensity
- MaxIntensityBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer.max
-
The buffer used when making a maximum-intensity projection
- MaxIntensityBuffer(Extent, VoxelsFactoryTypeBound<T>) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBuffer
- MaxIntensityBufferByte - Class in org.anchoranalysis.image.voxel.buffer.max
- MaxIntensityBufferByte(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferByte
- MaxIntensityBufferFloat - Class in org.anchoranalysis.image.voxel.buffer.max
- MaxIntensityBufferFloat(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferFloat
- MaxIntensityBufferInt - Class in org.anchoranalysis.image.voxel.buffer.max
- MaxIntensityBufferInt(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferInt
- MaxIntensityBufferShort - Class in org.anchoranalysis.image.voxel.buffer.max
- MaxIntensityBufferShort(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBufferShort
- MaxIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram
- MaxIntensityFromHistogram() - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.MaxIntensityFromHistogram
- MaxIntensityProjectionPair - Class in org.anchoranalysis.mpp.overlap
- MaxIntensityProjectionPair(BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, RegionMembershipWithFlags, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.overlap.MaxIntensityProjectionPair
- MaxNonZero - Class in org.anchoranalysis.plugin.mpp.bean.region
- MaxNonZero() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.MaxNonZero
- maxOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- MaxOverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
- MaxOverlapRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
- MaxOverlapRatio(double) - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
- MaxRatioRadii - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
- MaxRatioRadii() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.MaxRatioRadii
- MaxSliceArea - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
- MaxSliceArea() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MaxSliceArea
- MaxTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
- MaxTwoChannels(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxTwoChannels
- maxValue() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
-
The maximum value this type can represent.
- MaxWithConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
- MaxWithConstant - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
- MaxWithConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxWithConstant
- MaxWithConstant() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
- maybeAddOutputs() - Method in class org.anchoranalysis.launcher.options.outputs.ProcessOutputOptions
-
Processes any options that have been defined to add/remove change the outputs that are enabled.
- maybeAddPointToClosestEnd(Point3i) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
-
Adds the point to the closest end of the path....
- maybeCreateUserFriendlyException(Throwable) - Static method in class org.anchoranalysis.bean.xml.error.HelperFriendlyExceptions
-
Possibly replaces an exception with a more user-friendly description
- maybeDistanceCondition() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
- maybeSubdirectory(Optional<String>, ManifestDirectoryDescription, boolean) - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
-
Optionally creates a new context like with
InputOutputContext.subdirectory(java.lang.String, org.anchoranalysis.io.manifest.ManifestDirectoryDescription, boolean)but only if a directory-name is defined - mean() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
- mean() - Method in class org.anchoranalysis.math.arithmetic.RunningSum
-
Calculates the mean
- mean() - Method in class org.anchoranalysis.math.histogram.Histogram
- mean() - Method in class org.anchoranalysis.plugin.annotation.comparison.RangeSum
- mean() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
- mean(double) - Method in class org.anchoranalysis.math.arithmetic.RunningSum
-
Calculates the mean
- mean(double) - Method in class org.anchoranalysis.math.histogram.Histogram
-
calculates the mean after raising each histogram value to a power i.e.
- mean(double, double) - Method in class org.anchoranalysis.math.histogram.Histogram
-
calculates the mean of
(histogramVal - subtractVal)^power - Mean - Class in org.anchoranalysis.feature.bean.results
-
The mean of the results from a particular feature.
- Mean - Class in org.anchoranalysis.image.feature.histogram
- Mean<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
-
Arithmetic mean of a list of features
- Mean() - Constructor for class org.anchoranalysis.feature.bean.results.Mean
- Mean() - Constructor for class org.anchoranalysis.image.feature.histogram.Mean
- Mean() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.Mean
- MeanAcrossObjects<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
-
Calculates the mean of a feature applied to each connected component
- MeanAcrossObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.MeanAcrossObjects
- meanAndReset() - Method in class org.anchoranalysis.math.arithmetic.RunningSum
-
Calculate the mean and then reset to zero
- meanAndReset() - Method in class org.anchoranalysis.math.arithmetic.RunningSumCollection
-
Calculate the mean of each item and reset to zero.
- meanExecutionTimeFailed() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
-
Mean execution-time of failed jobs in milliseconds.
- meanExecutionTimeSuccess() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
-
Mean execution-time of successfully-completed jobs in milliseconds.
- MeanFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
- MeanFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.MeanFilter2D
- MeanFromAll - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
- MeanFromAll() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MeanFromAll
- MeanGeometric<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
- MeanGeometric() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.MeanGeometric
- meanGreaterEqualTo(int) - Method in class org.anchoranalysis.math.histogram.Histogram
- MeanIntensityBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer.mean
- MeanIntensityBuffer(VoxelsFactoryTypeBound<T>, Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
-
Simple constructor since no preprocessing is necessary.
- MeanIntensityByteBuffer - Class in org.anchoranalysis.image.voxel.buffer.mean
- MeanIntensityByteBuffer(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityByteBuffer
-
Simple constructor since no preprocessing is necessary.
- MeanIntensityDifference - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
- MeanIntensityDifference() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
- MeanIntensityDifference(double) - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
- MeanIntensityProjection - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
- MeanIntensityProjection() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.MeanIntensityProjection
- MeanIntensityShortBuffer - Class in org.anchoranalysis.image.voxel.buffer.mean
- MeanIntensityShortBuffer(Extent) - Constructor for class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityShortBuffer
-
Simple constructor since no preprocessing is necessary.
- meanNonZero() - Method in class org.anchoranalysis.math.histogram.Histogram
- meanOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- MeanRaisedToPower - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
The mean of the intensity raised to power
- MeanRaisedToPower() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
- MeanThreeChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Creates a new channel that is the mean of three input channels
- MeanThreeChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MeanThreeChannels
- meanXY() - Method in class org.anchoranalysis.spatial.point.RunningSumPoint
- Median - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Applies a median-filter with square kernel
- Median - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- Median() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
- Median() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Median
- MedianFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
- MedianFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter2D
- MedianFilter3D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
- MedianFilter3D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank.MedianFilter3D
- membershipForIndex(int) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
- membershipWithFlagsForIndex(int) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
- MemoCollection - Class in org.anchoranalysis.mpp.feature.mark
-
A collection of memoized marks on which energies can be derived.
- MemoCollection() - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoCollection
- MemoCollection(EnergySavedInd, EnergyStackWithoutParams, MarkCollection, EnergySchemeWithSharedFeatures) - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoCollection
- MemoCollection(MemoCollection) - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoCollection
- MemoForIndex - Interface in org.anchoranalysis.mpp.mark.voxelized.memo
- MemoList - Class in org.anchoranalysis.mpp.feature.mark
- MemoList() - Constructor for class org.anchoranalysis.mpp.feature.mark.MemoList
- MemoryUsageReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- MemoryUsageReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
- MemoryUtilities - Class in org.anchoranalysis.core.system
- merge() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
-
Merges
- merge(TypedEdge<ObjectVertex, PrioritisedVertex>) - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
- merge(ObjectCollection) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger
-
Merges all the objects together that are found in a collection
- merge(ObjectMask, ObjectMask) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger
-
Merges two objects together
- MergeBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
-
A base class for algorithms that merge object-masks
- MergeBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
- MergeBase.MergeObjects - Interface in org.anchoranalysis.plugin.image.bean.object.provider.merge
- mergeBoundingBoxes(Stream<ObjectMask>) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger
-
Merges all the bounding boxes of a stream of objects.
- mergeBoundingBoxes(Stream<BoundingBox>) - Static method in class org.anchoranalysis.spatial.box.BoundingBoxMerger
-
Merges all the bounding boxes in a stream.
- mergeBoundingBoxes(ObjectCollection) - Static method in class org.anchoranalysis.image.core.merge.ObjectMaskMerger
-
Merges all the bounding boxes of a collection of objects.
- MergeCandidate - Class in org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy
- MergeCandidate(ContiguousVoxelPath, ContiguousVoxelPath, Point3i, Point3i) - Constructor for class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
- Merged - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Evaluates the first-object in a pair only
- Merged() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Merged
- Merged(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Merged
- MERGED - org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
- MergedPairsFeatures - Class in org.anchoranalysis.image.feature.session.merged
-
The list of features that can be used in a
PairsTableCalculator - MergedPairsFeatures(FeatureList<FeatureInputPairObjects>) - Constructor for class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
-
Creates to only calculate pair features.
- MergedPairsFeatures(FeatureList<FeatureInputStack>, FeatureList<FeatureInputSingleObject>, FeatureList<FeatureInputPairObjects>) - Constructor for class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
-
Creates with features for single, pair and image as a whole.
- MergedPairsInclude - Class in org.anchoranalysis.image.feature.session.merged
- MergedPairsInclude() - Constructor for class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
- MergedPairsInclude(boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.feature.session.merged.MergedPairsInclude
- MergeGraph - Class in org.anchoranalysis.plugin.image.object.merge
-
A graph that stores each object as a vertex, where edges represent a neighborhood relation.
- MergeGraph(PayloadCalculator, UpdatableBeforeCondition, Optional<UnitConverter>, AssignPriority, Logger, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.MergeGraph
-
Constructor
- MergeGreedyToIncreaseObjectFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
-
Naive greedy merge strategy when any two neighboring objects are merged if it increases a feature.
- MergeGreedyToIncreaseObjectFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
- MergeLists - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
- MergeLists() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
- MergeMarkEllipse - Class in org.anchoranalysis.plugin.mpp.bean.proposer.merge
- MergeMarkEllipse() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
- mergeMultiplex(ObjectCollection, MergeBase.MergeObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
-
Merges either in a container, or altogether
- mergeObjects(ObjectCollection) - Method in interface org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase.MergeObjects
- MergePairs - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
-
Merges objects if a pair feature value satisfies a condition
- MergePairs() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
- MergeSpatialClusters - Class in org.anchoranalysis.plugin.ml.bean.cluster
-
Merges spatially-adjacent objects using the DBScan clustering algorithm.
- MergeSpatialClusters() - Constructor for class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
- MergeStrategy - Class in org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy
- MergeStrategy(int) - Constructor for class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeStrategy
- MergeToIncreaseObjectFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
-
Merges neighboring objects if it results in an increase in the average feature-value calculated on each single object
- MergeToIncreaseObjectFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
- MergeTwoCollectionsItemwise - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
-
Merges itemwise objects from two collections.
- MergeTwoCollectionsItemwise() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
- mergeViaZeroCheck(Channel, Channel, VoxelDataType, double) - Static method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
-
Creates a new channel which is a merged version of two input channels according to rules.
- MergeWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
-
Base class for object-merging strategies that involve calculating a feature.
- MergeWithFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
- MergeWithOptionalDistanceConstraint - Class in org.anchoranalysis.plugin.image.bean.object.provider.merge
-
Expands
MergeBaseby optionally imposing a maximum-distance requirement between objects that are possibly merged. - MergeWithOptionalDistanceConstraint() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
- messageLogger() - Method in class org.anchoranalysis.core.log.Logger
-
Where messages logged to
- MessageLogger - Interface in org.anchoranalysis.core.log
-
Logs messages (strings) somewhere.
- MessageLoggerList - Class in org.anchoranalysis.experiment.log
- MessageLoggerList(Stream<StatefulMessageLogger>) - Constructor for class org.anchoranalysis.experiment.log.MessageLoggerList
- metadataAggregated(NamedFeatureStore<FeatureInputResults>) - Method in class org.anchoranalysis.feature.io.results.ResultsWriterMetadata
-
Derives metadata for the aggregated CSV output, if enabled.
- metadataNonAggregated() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterMetadata
-
Derives metadata for the non-aggregated CSV output.
- MICRO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
- midpoint() - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
A mid-point in the bounding box, in the exact half way point between (crnr+extent)/2.
- midPointBetween(Point3d, Point3d) - Static method in class org.anchoranalysis.spatial.point.Point3d
- min() - Method in class org.anchoranalysis.plugin.annotation.comparison.RangeSum
- min(boolean) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- min(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Point3d
-
Element-wise minimum between this point and another
- min(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i
-
Element-wise minimum between this point and another
- min(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Point3d
-
Element-wise minimum between this point and another
- Min - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- Min() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Min
- MIN_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.FloatVoxelType
- MIN_VALUE - Static variable in class org.anchoranalysis.image.voxel.datatype.SignedShortVoxelType
- minArea() - Method in class org.anchoranalysis.mpp.overlap.MaxIntensityProjectionPair
- minAsInt(ToIntFunction<ObjectMask>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Finds the minimum value of a function applied to each object in the collection.
- minDistanceMaxToHeadTail(Point3i, List<ContiguousVoxelPath>) - Static method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.FindMinimumDistance
-
The maximum-distance of a point to the closest contiguous-path
- MinFeatureAsIndividual - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
- MinFeatureAsIndividual() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.MinFeatureAsIndividual
- MinFeatureIntersectingObjectsAboveThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
-
1.
- MinFeatureIntersectingObjectsAboveThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.MinFeatureIntersectingObjectsAboveThreshold
- MinimaImposition - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
- MinimaImposition() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImposition
- MinimaImpositionGrayscaleReconstruction - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
- MinimaImpositionGrayscaleReconstruction() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
- MinimalExecutionTimeStatsReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- MinimalExecutionTimeStatsReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
- Minimum - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Ratio of first-object to second-object in a pair
- Minimum - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
The minimum value of one or more {#link org.anchoranalysis.image.bean.threshold.CalculateLevel}
- Minimum<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.list
- Minimum() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Minimum
- Minimum() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Minimum
- Minimum() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.list.Minimum
- Minimum(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Minimum
- MINIMUM - org.anchoranalysis.core.index.bounded.BoundChangeEvent.BoundType
- MinimumDistanceByDimension - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
-
The minimum distance in any one particular axis-aligned direction (i.e.
- MinimumDistanceByDimension() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.MinimumDistanceByDimension
- MinimumFilter - Class in org.anchoranalysis.plugin.fiji.bean.channel.provider
- MinimumFilter() - Constructor for class org.anchoranalysis.plugin.fiji.bean.channel.provider.MinimumFilter
- minNumPoints() - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresViaNormalEquationBase
- minOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- MinTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
- MinTwoChannels(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinTwoChannels
- minVal - Variable in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- minValue() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
-
The minimum value this type can represent.
- MinWithConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
- MinWithConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinWithConstant
- MockFeatureWithCalculation - Class in org.anchoranalysis.test.feature.plugins.mockfeature
-
A feature that returns the number-of-voxels in an object by using am internal mock-calculation.
- MockFeatureWithCalculation() - Constructor for class org.anchoranalysis.test.feature.plugins.mockfeature.MockFeatureWithCalculation
- MockFeatureWithCalculationFixture - Class in org.anchoranalysis.test.feature.plugins.mockfeature
-
Creates a mock-feature which used a mock
FeatureCalculationunder the hood - Mode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- Mode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Mode
- MonitoredSequentialExecutor<T> - Class in org.anchoranalysis.experiment.task.processor
-
Runs executes sequence of jobs/tasks/whatever monitoring various pieces of information - how many have run? - how many successful/failed? - how long did execution take? - etc.
- MonitoredSequentialExecutor(Predicate<T>, Function<T, String>, Optional<MessageLogger>, boolean) - Constructor for class org.anchoranalysis.experiment.task.processor.MonitoredSequentialExecutor
- MontageSlices - Class in org.anchoranalysis.plugin.imagej.bean.stack.provider
- MontageSlices() - Constructor for class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
- moreThanOneObj() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.AnnotationComparisonAssigner
-
Can more than one object exist?
- moreThanOneObj() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
- moreThanOneObj() - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.MaskIntersectionAssigner
- MorphologicalDilation - Class in org.anchoranalysis.image.voxel.object.morphological
- MorphologicalErosion - Class in org.anchoranalysis.image.voxel.object.morphological
- MorphologicalIterations - Class in org.anchoranalysis.plugin.image.feature.bean.morphological
-
Specifies a certain number of iterations of the morphological operations of dilation and erosion
- MorphologicalIterations() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
- MorphologicalOperation - Class in org.anchoranalysis.plugin.imagej.bean.mask.provider
-
Applies an ImageJ (2D) morphological operation to each slice
- MorphologicalOperation() - Constructor for class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
- MorphologicalOperatorBase - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
-
Base class for performing morphological operations
- MorphologicalOperatorBase() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
- moveAcceptedToAvailable(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
- moveAvailableToAccepted(Set<Mark>) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
- MovieFromSlices - Class in org.anchoranalysis.plugin.image.task.bean.slice
- MovieFromSlices() - Constructor for class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- MPPBean<T> - Class in org.anchoranalysis.mpp.bean
- MPPBean() - Constructor for class org.anchoranalysis.mpp.bean.MPPBean
- MPPInitParams - Class in org.anchoranalysis.mpp.bean.init
- MPPInitParams(ImageInitParams, SharedObjects) - Constructor for class org.anchoranalysis.mpp.bean.init.MPPInitParams
- MPPInitParamsFactory - Class in org.anchoranalysis.mpp.io.input
- MPPProvider<T,S> - Class in org.anchoranalysis.mpp.bean.provider
- MPPProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.MPPProvider
- Mser - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Applies the MSER algorithm from imglib2
- Mser() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
- mult(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
- multConstant(double) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
- MultiBufferSized - Class in org.anchoranalysis.plugin.io.multifile.buffer
- MultiBufferSized(Stack, SizeExtents) - Constructor for class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
- MultiFileReader - Class in org.anchoranalysis.plugin.io.bean.stack.reader
- MultiFileReader() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
- MultiFileReaderOpenedRaster - Class in org.anchoranalysis.plugin.io.multifile
- MultiFileReaderOpenedRaster(StackReader, ParsedFilePathBag) - Constructor for class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
- MultiInput - Class in org.anchoranalysis.mpp.io.input
- MultiInput(String, ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.MultiInput
- MultiInput(ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.MultiInput
- MultiInputManager - Class in org.anchoranalysis.mpp.io.bean.input
- MultiInputManager() - Constructor for class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- MultiInputManager(String, InputManager<? extends ProvidesStackInput>) - Constructor for class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- MultiInputManagerQuick - Class in org.anchoranalysis.plugin.quick.bean.input
-
A multi-input manager that makes various assumptions, so it can be more quickly specified.
- MultiInputManagerQuick() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
- MultiInputSubMap<T> - Interface in org.anchoranalysis.mpp.io.input
-
a sub-item of multi-input which: 1.
- MultiLevelAnd - Class in org.anchoranalysis.io.output.enabled.multi
-
Outputs are enabled if they are contained in both of two
MultiLevelOutputEnableds. - MultiLevelAnd(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelAnd
-
Creates using two
MultiLevelOutputEnableds. - MultiLevelBinary - Class in org.anchoranalysis.io.output.enabled.multi
- MultiLevelBinary(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
- MultiLevelNot - Class in org.anchoranalysis.io.output.enabled.multi
-
The complement of an existing
MultiLevelOutputEnabledwhere disabled outputs are enabled, and vice-versa. - MultiLevelNot(MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
- MultiLevelOr - Class in org.anchoranalysis.io.output.enabled.multi
-
Outputs are enabled if they are contained in either of two
MultiLevelOutputEnableds. - MultiLevelOr(MultiLevelOutputEnabled, MultiLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.multi.MultiLevelOr
-
Creates using two
MultiLevelOutputEnableds. - MultiLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.multi
-
Whether an output is enabled or not in a context of hierarchy of different rules for outputting.
- MultiLevelRecordedOutputs - Class in org.anchoranalysis.io.output.recorded
-
Like
RecordedOutputsbut accepts two levels, first and second, like in aMultiLevelRecordedOutputs. - MultiLevelRecordedOutputs() - Constructor for class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
- MultiName - Interface in org.anchoranalysis.feature.io.name
-
A name that that uniquely identifies an entity, and is composed of two parts.
- MultiNameFactory - Class in org.anchoranalysis.feature.io.name
-
Creates
MultiName. - MultipleComparer - Class in org.anchoranalysis.annotation.io.bean.comparer
-
Allows comparison of an annotation with multiple other entities.
- MultipleComparer() - Constructor for class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
- MultipleFileTypeGenerator<T> - Interface in org.anchoranalysis.io.generator
-
A
Generatorthat creates multiple different file-types. - multipleProcessors(int, int) - Static method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
-
Creates a plan for a multiple CPU-processors
- multipleSeries() - Method in class org.anchoranalysis.plot.index.PlotIndexBase
- multiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters
-
Multiplexes between the
selectiveandpermissivewriters based on a flag. - Multiply<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
- Multiply() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Multiply
- multiplyBy(double) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic
-
Multiplies the value of all voxels by a factor
- multiplyBy(ObjectMask, double) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic
-
Multiplies each voxel by constant factor but only for voxels inside an object-mask
- MultiplyByConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
- MultiplyByConstant() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
- MultiplyByConstant(Feature<T>, double) - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.MultiplyByConstant
- MultiplyConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
- MultiplyConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyConstant
- MultiplyTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
- MultiplyTwoChannels(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyTwoChannels
- MutableDirectory - Class in org.anchoranalysis.io.manifest.directory
-
An entry for a directory in the manifest, to which outputs and sub-directories can be later added.
- MutableDirectory() - Constructor for class org.anchoranalysis.io.manifest.directory.MutableDirectory
- MutableDirectory(MutableDirectory) - Constructor for class org.anchoranalysis.io.manifest.directory.MutableDirectory
N
- name() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
- name() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- name() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
- name() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
- name() - Method in class org.anchoranalysis.plugin.io.manifest.CoupledManifests
- name() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
- name() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
- NamedBean<T extends AnchorBean<?>> - Class in org.anchoranalysis.bean
-
A bean with an associated textual name.
- NamedBean() - Constructor for class org.anchoranalysis.bean.NamedBean
- NamedBean(String, T) - Constructor for class org.anchoranalysis.bean.NamedBean
- NamedChannel - Class in org.anchoranalysis.plugin.image.task.grouped
- NamedChannel(String, Channel) - Constructor for class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
- NamedChannels - Class in org.anchoranalysis.plugin.io.bean.input.channel
-
An image viewed as a named set of channels
- NamedChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
- NamedChannelsAppend - Class in org.anchoranalysis.plugin.io.bean.input.channel
- NamedChannelsAppend() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- NamedChannelsBase - Class in org.anchoranalysis.plugin.io.bean.input.channel
-
Parent for all the
NamedChannelsclasses - NamedChannelsBase() - Constructor for class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsBase
- NamedChannelsQuick - Class in org.anchoranalysis.plugin.quick.bean.input
-
A particular type of NamedChannels which allows easier input of data, making several assumptions.
- NamedChannelsQuick() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
- NamedFeatureCalculateException - Exception in org.anchoranalysis.feature.calculate
-
A feature-calculation exception that occurs in a particular named feature, or else a general message of failure.
- NamedFeatureCalculateException(Exception) - Constructor for exception org.anchoranalysis.feature.calculate.NamedFeatureCalculateException
-
Creates with a calculation error that doesn't pertain to any particular feature.
- NamedFeatureCalculateException(String) - Constructor for exception org.anchoranalysis.feature.calculate.NamedFeatureCalculateException
-
Creates with a general failure message that doesn't pertain to any particular feature.
- NamedFeatureCalculateException(String, String) - Constructor for exception org.anchoranalysis.feature.calculate.NamedFeatureCalculateException
-
Creates with a failure message associated with a particular feature.
- NamedFeatureCalculatorMulti<T extends FeatureInput> - Class in org.anchoranalysis.image.feature.evaluator
-
A
FeatureCalculatorMultiwith associated feature-names - NamedFeatureCalculatorMulti(FeatureCalculatorMulti<T>, FeatureNameList) - Constructor for class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
- NamedFeatureStore<T extends FeatureInput> - Class in org.anchoranalysis.feature.list
- NamedFeatureStore() - Constructor for class org.anchoranalysis.feature.list.NamedFeatureStore
- NamedFeatureStoreFactory - Class in org.anchoranalysis.feature.list
- NamedFiles - Class in org.anchoranalysis.plugin.io.bean.input.files
-
File-paths
- NamedFiles() - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
- NamedFiles(FilesProvider) - Constructor for class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
- NamedPath - Class in org.anchoranalysis.io.output.path.prefixer
-
A path and associated name.
- NamedPath(String, Path) - Constructor for class org.anchoranalysis.io.output.path.prefixer.NamedPath
- NamedProvider<T> - Interface in org.anchoranalysis.core.identifier.provider
-
A collection of named-elements that provides an element for a given name.
- NamedProviderBridge<S,T> - Class in org.anchoranalysis.core.identifier.provider
- NamedProviderBridge(NamedProvider<S>, CheckedFunction<S, T, ? extends Exception>) - Constructor for class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
- NamedProviderBridge(NamedProvider<S>, CheckedFunction<S, T, ? extends Exception>, boolean) - Constructor for class org.anchoranalysis.core.identifier.provider.NamedProviderBridge
- NamedProviderCombine<T> - Class in org.anchoranalysis.core.identifier.provider
- NamedProviderCombine() - Constructor for class org.anchoranalysis.core.identifier.provider.NamedProviderCombine
- NamedProviderGetException - Exception in org.anchoranalysis.core.identifier.provider
- NamedProviderGetException(String, Throwable) - Constructor for exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
- NamedProviderOutputter<T> - Class in org.anchoranalysis.io.generator.collection
-
Outputs entities from a
NamedProviderinto a directory using the names of each entity for a corresponding generated file. - NamedProviderOutputter(NamedProvider<T>, Generator<T>, OutputterChecked) - Constructor for class org.anchoranalysis.io.generator.collection.NamedProviderOutputter
- NamedProviderStore<T> - Interface in org.anchoranalysis.core.identifier.provider.store
-
A provider, in which items can also be added.
- NamedStacks - Class in org.anchoranalysis.image.core.stack
-
A set of image-stacks each with a name
- NamedStacks() - Constructor for class org.anchoranalysis.image.core.stack.NamedStacks
- NamedStacksSupplier - Interface in org.anchoranalysis.image.core.stack
- NamedStacksUniformSize - Class in org.anchoranalysis.image.core.stack
-
Like a @{link
NamedStacksbut enforces a condition that all stacks must have the same dimensions - NamedStacksUniformSize() - Constructor for class org.anchoranalysis.image.core.stack.NamedStacksUniformSize
- nameForPropValue(Double) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
- nameForPropValue(Double) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
- nameForPropValue(Integer) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
- nameForPropValue(Integer) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
- nameForPropValue(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
- nameForPropValue(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
- nameForPropValue(T) - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty
-
Converts a particular value to a string representation
- nameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
-
Constructs a full name from the output format string and an index
- nameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
- nameFromOutputFormatString(String, String) - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
- NameValue<T> - Interface in org.anchoranalysis.core.identifier.name
-
An object that has an associated textual name and value
- NameValueSet<T> - Class in org.anchoranalysis.core.identifier.provider
- NameValueSet() - Constructor for class org.anchoranalysis.core.identifier.provider.NameValueSet
- NameValueSet(Iterable<? extends NameValue<T>>) - Constructor for class org.anchoranalysis.core.identifier.provider.NameValueSet
- NANO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
- negative() - Method in class org.anchoranalysis.image.core.orientation.Orientation
- negative() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- negative() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
- negative() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
- negative() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
- negative() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
- NeighborGraph - Class in org.anchoranalysis.image.voxel.neighborhood
- Neighborhood - Interface in org.anchoranalysis.image.voxel.neighborhood
- NeighborhoodCondition - Class in org.anchoranalysis.plugin.image.object.merge.condition
-
A condition placed to determine if two objects could be potential neighbors are not (i.e.
- NeighborhoodCondition(boolean, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
- NeighborhoodFactory - Class in org.anchoranalysis.image.voxel.neighborhood
-
Creates either a big voxel-neighborhood or a small voxel-neighborhood.
- newlinesBeforeError() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
-
if true, then some extra newlines are inserted before error messages
- newTemplateMark() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
- next() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble.DoubleRange
- nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
- nextIndex(int) - Method in interface org.anchoranalysis.core.index.bounded.BoundedRangeIncomplete
- nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
- nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
- nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
- nextIndex(int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
- nextValue() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
- NoAnnealing - Class in org.anchoranalysis.plugin.mpp.segment.bean.annealing
- NoAnnealing() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.annealing.NoAnnealing
- noInterpolation() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorFactory
- None - Class in org.anchoranalysis.image.bean.interpolator
- None - Class in org.anchoranalysis.io.output.bean.enabled
-
No outputs are enabled.
- None() - Constructor for class org.anchoranalysis.image.bean.interpolator.None
- None() - Constructor for class org.anchoranalysis.io.output.bean.enabled.None
- NONE - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
- NoneExcept - Class in org.anchoranalysis.io.output.bean.rules
-
All outputs are disabled except particular ones.
- NoneExcept() - Constructor for class org.anchoranalysis.io.output.bean.rules.NoneExcept
- NoneExcept(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.NoneExcept
-
Create with first-level output names
- NonEmpty - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a collection must have at least one item.
- nonExistingItem(String) - Static method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
- nonExistingItem(String, String) - Static method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
- NonMaximaSuppression<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
A strategy for reducing elements that greedily removes any element with a strong overlap with another.
- NonMaximaSuppression() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
- NonNegative - Annotation Type in org.anchoranalysis.bean.annotation
-
The bean-field should have a value
>= 0 - noOverlapWith(Mark, int) - Method in interface org.anchoranalysis.mpp.mark.QuickOverlapCalculation
-
A quick (computationally-efficient) test to see if we can reject the possibility of overlap
- noPadding() - Method in class org.anchoranalysis.image.bean.spatial.Padding
- normalisedRadii(Ellipsoid, Optional<Resolution>) - Static method in class org.anchoranalysis.mpp.mark.conic.EllipsoidUtilities
- normalize() - Method in class org.anchoranalysis.spatial.point.Vector3d
- NormalizeByConstant - Class in org.anchoranalysis.plugin.image.feature.bean.score
- NormalizeByConstant() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
- NormalizeByMax - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
This assumes the histograms correspond to the energy channels exactly (in terms of indexing)
- NormalizeByMax() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByMax
- NormalizeDifferenceToMedian - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Corrects a channel in the following way
- NormalizeDifferenceToMedian() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
- NormalizedPath - Class in org.anchoranalysis.plugin.io.bean.descriptivename
-
Uses the normalized path (always with forward slashes) of each file as it's descriptive-name
- NormalizedPath() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.NormalizedPath
- NormalizedRange<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range.feature
-
The range of two feature values (i.e.
- NormalizedRange() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.feature.NormalizedRange
- NormalizeObjectIntensity - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Rewrites the intensity for each object-mask (assume no overlap) so that its mean is 128
- NormalizeObjectIntensity() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeObjectIntensity
- NoSharedState - Class in org.anchoranalysis.experiment.task
-
Fake shared-state to use to indicate none exists (for type safety)
- Not - Class in org.anchoranalysis.plugin.mpp.bean.check
- Not() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.Not
- NotFound<T> - Class in org.anchoranalysis.annotation.io.image.findable
-
A negative-result when an object is NOT found at a particular location.
- NotFound(Path, String) - Constructor for class org.anchoranalysis.annotation.io.image.findable.NotFound
- notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.buffer.PredicateBufferBinary
-
Notifies the processor that there has been a change in slice (z global coordinate)
- notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinary
-
Notifies the processor that there has been a change in slice (z global coordinate)
- notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryMixed
-
Notifies the processor that there has been a change in slice (z global coordinate)
- notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryWithoutOffset
-
Notifies the processor that there has been a change in slice (z global coordinate)
- notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferTernary
-
Notifies the processor that there has been a change in slice (z global coordinate)
- notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferUnary
-
Notifies the processor that there has been a change in slice (z global coordinate)
- notifyChangeSlice(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint
-
Notifies the processor that there has been a change in z-coordinate
- notifyChangeY(int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint
-
Notifies the processor that there has been a change in y-coordinate
- notifyChangeZ(int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor
-
Notifies the processor that there has been a change in z-coordinate
- notifyChangeZ(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute
-
Notifies the processor that there has been a change in z-coordinate
- notifyChangeZ(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
- notifyChangeZ(int, int, UnsignedByteBuffer) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked
-
Notifies the processor that there has been a change in z-coordinate
- notifyChangeZ(int, int, UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
- notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.AndKernel
- notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.ConditionalKernel
- notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodBase
- notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.count.CountKernelNeighborhoodMask
- notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.density.DensityKernel
- notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.density.MaxDensityKernel3
- notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
- notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
- notifyZChange(LocalSlices, int) - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3NeighborMatchValue
- NoTimeSeries - Class in org.anchoranalysis.io.imagej.bean.stack.writer
-
Base class for
ImageJRasterWriterthat doesn't support writing time-series as a stack. - NoTimeSeries() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.NoTimeSeries
- NotInContainer - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
-
Filters objects to keep only those which are NOT in the container.
- NotInContainer() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.NotInContainer
- NotTouchingSceneBorder - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Keeps only objects that are not adjacent to the scene-border (i.e.
- NotTouchingSceneBorder() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
- NullInitParams - Class in org.anchoranalysis.bean.initializable.params
- NullMessageLogger - Class in org.anchoranalysis.core.log
-
Does nothing with (i.e.
- NullMessageLogger() - Constructor for class org.anchoranalysis.core.log.NullMessageLogger
- NullParamsBean<T> - Class in org.anchoranalysis.bean
-
A base class for beans that require initialization but the initializations needs no parameters.
- NullParamsBean() - Constructor for class org.anchoranalysis.bean.NullParamsBean
- NullReporter<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
-
Dummy reporter that takes no action.
- NullReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
- NUMBER_DIGITS_IN_OUTPUT - Static variable in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
- NUMBER_ELEMENTS_WRITTEN_ERRORED - Static variable in class org.anchoranalysis.io.output.writer.WriterRouterErrors
- NUMBER_ELEMENTS_WRITTEN_NOT_ALLOWED - Static variable in class org.anchoranalysis.io.output.writer.CheckIfAllowed
- numberBits() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
-
The number of bits required to represent a voxel.
- numberBorderPixels(ObjectMask, OutlineKernelParameters) - Static method in class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder
- numberChannels() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
-
A list of channel-names or null if they are not available.
- numberChannels() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
- NumberChannels - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
- NumberChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.NumberChannels
- numberCompletedFailed() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
- numberCompletedFailureJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- numberCompletedJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- numberCompletedSuccess() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
- numberCompletedSuccessfullyJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.Orientation
- numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
- numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
- numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.OrientationIdentity
- numberDimensions() - Method in class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
- numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
- numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- numberDimensions() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
- numberDimensions() - Method in class org.anchoranalysis.mpp.mark.Mark
- numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.PointList
- numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
- numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
- numberDimensions() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
- numberDimensions() - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAngle2D
- numberDimensions() - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAngle3D
- numberDimensions() - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAxisAngle
- numberDimensions() - Method in class org.anchoranalysis.spatial.rotation.factory.RotationMatrixFactory
-
The dimensionality of the rotation-matrix.
- numberDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
-
Number of output-names that were not enabled.
- NumberDistinctValues - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- NumberDistinctValues() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.NumberDistinctValues
- numberEdges() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
The number of edges in the graph.
- numberEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
-
Number of output-names that were enabled.
- numberExecutingJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- numberFoundFrom(Set<Contour>) - Method in class org.anchoranalysis.plugin.points.contour.ContourList
- numberFrames() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
- numberFrames() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- numberFrames() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
- numberFrames() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
- numberGPUs() - Method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
- numberImageFeatures() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
- NumberIntersectingObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
- NumberIntersectingObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjects
- NumberIntersectingObjectsAboveThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
-
1.
- NumberIntersectingObjectsAboveThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjectsAboveThreshold
- numberItemsCurrentlyStored() - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
-
Number of items currently stored in cache
- NumberIterations - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
- NumberIterations() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
- NumberIterations(int) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
- numberManifests() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
- NumberMarks - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.collection
- NumberMarks - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.all
- NumberMarks() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.collection.NumberMarks
- NumberMarks() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.NumberMarks
- NumberMarksFromManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
- NumberMarksFromManifest() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.NumberMarksFromManifest
- numberMatches() - Method in class org.anchoranalysis.image.core.object.MatchedObject
- NumberNeighboringVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
-
Calculates the number of voxels on the object that have a neighbor (according to a binary-mask on an energy-channel)
- NumberNeighboringVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
- numberNonNullConverters() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- numberNotCompleted() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
-
Number of jobs that have not been completed.
- NumberObjects - Class in org.anchoranalysis.plugin.image.feature.bean.object.collection
- NumberObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.collection.NumberObjects
- numberOngoingJobs() - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- numberPaired() - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
- numberPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
- numberPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- numberPairFeatures() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
- NumberPoints - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
- NumberPoints() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.NumberPoints
- numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- numberRegions() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- numberRegions() - Method in class org.anchoranalysis.mpp.mark.Mark
- numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.PointList
- numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
- numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
- numberRegions() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
- NumberRemovedVoxelsAfterClosing - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
-
How many pixels are removed after a morphological closing operation on the object-mask.
- NumberRemovedVoxelsAfterClosing() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
- numberSeries() - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
- numberSeries() - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
- numberSingleFeatures() - Method in class org.anchoranalysis.image.feature.session.merged.MergedPairsFeatures
- numberSlicesProcessed() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
- numberTotalScheduledJobs() - Method in class org.anchoranalysis.experiment.task.TaskStatistics
-
Total number of scheduled jobs.
- numberUnassigned(boolean) - Method in interface org.anchoranalysis.annotation.io.assignment.Assignment
- numberUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentMaskIntersection
- numberUnassigned(boolean) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- numberUniqueColors() - Method in interface org.anchoranalysis.core.color.ColorIndex
- numberUniqueColors() - Method in class org.anchoranalysis.core.color.ColorIndexModulo
- numberUniqueColors() - Method in class org.anchoranalysis.core.color.ColorList
- numberUniqueColors() - Method in class org.anchoranalysis.core.color.SingleColor
- numberVertices() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
The number of vertices in the graph.
- numberVoxels() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
- NumberVoxels - Class in org.anchoranalysis.image.feature.bean.object.single
- NumberVoxels() - Constructor for class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
- NumberVoxelsAtBorder - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.border
- NumberVoxelsAtBorder() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.border.NumberVoxelsAtBorder
- numberVoxelsOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
The number of "ON" voxels on the object-mask
- numFrames() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
- numGroups() - Method in class org.anchoranalysis.plugin.annotation.bean.label.GroupedAnnotationLabels
- numImagesAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- numImagesTotal() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- numImagesWithAcceptedAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- numImagesWithoutAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- numImagesWithSkippedAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- numProbMap() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- numRegions() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
- numSlices() - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByRegion
- numSlices() - Method in interface org.anchoranalysis.mpp.voxel.partition.VoxelPartition
- numSlices() - Method in class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
- numSlices() - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
- NumTouchingVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
-
A scheme for counting the touching voxels by intersection of object-masks
- NumTouchingVoxelFaces() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumTouchingVoxelFaces
- NumTouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
-
A scheme for counting touching voxels.
- NumTouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.NumTouchingVoxels
- numUnassignedLeft() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- numUnassignedRight() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
O
- ObjectAggregationBase<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
-
Calculates a feature for a set of objects using this stack as a energy-stack, and aggregates.
- ObjectAggregationBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
- ObjectAsPoints - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
- ObjectAsPoints() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
- ObjectCollection - Class in org.anchoranalysis.image.voxel.object
-
A collection of
ObjectMask - ObjectCollection() - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollection
-
Creates with no objects
- ObjectCollection(Stream<ObjectMask>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollection
-
Creates with elements from a stream
- ObjectCollectionFactory - Class in org.anchoranalysis.image.voxel.object.factory
-
Creates
ObjectCollectionusing various utility and helper methods - ObjectCollectionProvider - Class in org.anchoranalysis.image.bean.provider
- ObjectCollectionProvider() - Constructor for class org.anchoranalysis.image.bean.provider.ObjectCollectionProvider
- ObjectCollectionProviderFilterBase - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
- ObjectCollectionProviderFilterBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
- ObjectCollectionProviderMorphological - Class in org.anchoranalysis.plugin.image.bean.object.provider.morphological
- ObjectCollectionProviderMorphological() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
- ObjectCollectionProviderUnary - Class in org.anchoranalysis.image.bean.provider
-
Base class for
ObjectCollectionProviderthat take aobjectsbean-field of same type as provided. - ObjectCollectionProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
- ObjectCollectionProviderWithFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
- ObjectCollectionProviderWithFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
- ObjectCollectionRTree - Class in org.anchoranalysis.image.voxel.object
-
An R-Tree of object-masks (indexed via a derived bounding-box).
- ObjectCollectionRTree(ObjectCollection) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
-
Creates an r-tree for particular objects.
- ObjectCollectionWithProperties - Class in org.anchoranalysis.image.core.object.properties
-
Like an
ObjectCollectionbut each object has associated properties. - ObjectCollectionWithProperties() - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
- ObjectCollectionWithProperties(Stream<ObjectWithProperties>) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
- ObjectCollectionWithProperties(ObjectCollection) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
- ObjectCollectionWithProperties(ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
- ObjectCollectionWithPropertiesFactory - Class in org.anchoranalysis.image.core.object.properties
- ObjectComparer - Class in org.anchoranalysis.plugin.annotation.bean.comparer
-
An object-collection to be used to compare against something
- ObjectComparer() - Constructor for class org.anchoranalysis.plugin.annotation.bean.comparer.ObjectComparer
- objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in class org.anchoranalysis.image.voxel.extracter.Base
- objectCopyTo(ObjectMask, Voxels<T>, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
-
Copies an area corresponding to an object-mask to another
Voxels - ObjectDrawAttributes - Class in org.anchoranalysis.overlay.writer
-
A means of extracting attributes associated with a particular object (e.g.
- ObjectDrawAttributes(ColorIndex) - Constructor for class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
-
Creates with a specific color-index and uses the iteration-index as both the ID and color-ID
- ObjectDrawAttributes(ColorIndex, IdentifierGetter<ObjectWithProperties>, IdentifierGetter<ObjectWithProperties>) - Constructor for class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
- ObjectDrawAttributesFactory - Class in org.anchoranalysis.overlay.writer
- ObjectFilter - Class in org.anchoranalysis.image.bean.object
- ObjectFilter() - Constructor for class org.anchoranalysis.image.bean.object.ObjectFilter
- ObjectFilterCombine - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
-
A filter that combines other filters (in a list)
- ObjectFilterCombine() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine
- ObjectFilterPredicate - Class in org.anchoranalysis.plugin.image.bean.object.filter
-
Uses a predicate to make a decision whether to keep objects or not.
- ObjectFilterPredicate() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
- ObjectFilterRelation - Class in org.anchoranalysis.plugin.image.bean.object.filter
-
An independent object-filter that uses a relation in its predicate.
- ObjectFilterRelation() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
- objectFor(T) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask
-
An object-mask for a given element.
- ObjectInputStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize
- ObjectInputStreamDeserializer() - Constructor for class org.anchoranalysis.core.serialize.ObjectInputStreamDeserializer
- ObjectIntersectionRemover - Class in org.anchoranalysis.plugin.image.object
- ObjectMask - Class in org.anchoranalysis.image.voxel.object
-
An object expressed in voxels, bounded within overall space.
- ObjectMask(BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
- ObjectMask(BoundedVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
-
Creates an object-mask to correspond to bounded-voxels.
- ObjectMask(BoundedVoxels<UnsignedByteBuffer>, BinaryValues) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
- ObjectMask(Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
-
Creates an object-mask with a corner at the origin (i.e.
- ObjectMask(BoundingBox) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
-
Creates an object-mask to corresponding to a bounding-box with all pixels off (0)
- ObjectMask(BoundingBox, BinaryVoxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
- ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
- ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValues) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
- ObjectMask(BoundingBox, Voxels<UnsignedByteBuffer>, BinaryValuesByte) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMask
- ObjectMaskMerger - Class in org.anchoranalysis.image.core.merge
-
Merges one or more
ObjectMasks into a single object - ObjectMaskStream - Class in org.anchoranalysis.image.voxel.object
-
A custom "stream" like class for various functional-programming operations on
ObjectCollection - ObjectMaskStream(ObjectCollection) - Constructor for class org.anchoranalysis.image.voxel.object.ObjectMaskStream
- ObjectMatcher - Class in org.anchoranalysis.image.bean.object
-
Matches an object with other objects.
- ObjectMatcher() - Constructor for class org.anchoranalysis.image.bean.object.ObjectMatcher
- ObjectOutputStreamGenerator<T extends Serializable> - Class in org.anchoranalysis.io.generator.serialized
- ObjectOutputStreamGenerator() - Constructor for class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
- ObjectOutputStreamGenerator(Optional<String>) - Constructor for class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
- ObjectRadiusStandardDeviation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
- ObjectRadiusStandardDeviation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
- objects() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- objects() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
-
All objects stored in the r-tree (whose order corresponds to indices in
delegate - objects() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- objects(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
- OBJECTS - Static variable in class org.anchoranalysis.mpp.segment.define.OutputterDirectories
-
Where collections of objects are typically placed in a define-experiment output
- objectsAreAllInside(Extent) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- ObjectSerializerPeriodicReporter<T extends Serializable> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- ObjectSerializerPeriodicReporter(String) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
- objectsForThumbnail(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
- objectsForThumbnail(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
- objectsForThumbnail(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
-
Selects objects from an input that will be used for thumbnail generation
- ObjectsFromConnectedComponentsFactory - Class in org.anchoranalysis.image.voxel.object.factory
-
Creates a
ObjectCollectionfrom the connected-components of a mask or binary-voxels. - ObjectsFromConnectedComponentsFactory() - Constructor for class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
- ObjectsFromConnectedComponentsFactory(boolean) - Constructor for class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
- ObjectsFromConnectedComponentsFactory(boolean, int) - Constructor for class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
- ObjectsFromConnectedComponentsFactory(int) - Constructor for class org.anchoranalysis.image.voxel.object.factory.ObjectsFromConnectedComponentsFactory
- objectsFromOverlays(OverlayCollection) - Static method in class org.anchoranalysis.overlay.collection.OverlayCollectionObjectFactory
-
Creates objects from whatever Overlays are found in the collection *
- ObjectsToCompare - Class in org.anchoranalysis.plugin.annotation.comparison
- ObjectsToCompare(ObjectCollection, ObjectCollection) - Constructor for class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
- objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
-
The objects to draw (without any colors) on the background
- objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
- objectsToDraw(Dimensions) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
- ObjectVertex - Class in org.anchoranalysis.plugin.image.object.merge
-
A vertex in a merge graph representing an object (and and an associated payload)
- ObjectVertex(ObjectMask, double) - Constructor for class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
- ObjectWithEllipse - Class in org.anchoranalysis.plugin.points.calculate.ellipse
- ObjectWithEllipse(ObjectMask, Ellipse) - Constructor for class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
- ObjectWithMaximumFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
Finds the object with the maximum feature-value from a collection.
- ObjectWithMaximumFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeature
- ObjectWithMaximumFeatureFromEachMatchedCollection - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
Finds the object with the maximum feature among a group of matches for each object.
- ObjectWithMaximumFeatureFromEachMatchedCollection() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
- ObjectWithProperties - Class in org.anchoranalysis.image.core.object.properties
-
An
ObjectMaskwith associated key-value properties. - ObjectWithProperties(ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- ObjectWithProperties(ObjectMask, Map<String, Object>) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- ObjectWithProperties(BoundingBox) - Constructor for class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- obtain(int, AggregateReceiver<T>, PeriodTriggerBank<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
- obtain(int, PeriodReceiver<S>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodTriggerBank
- of(boolean) - Static method in class org.anchoranalysis.image.voxel.neighborhood.NeighborhoodFactory
-
Gets an appropriate neighborhood
- of(boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.SelectDimensionsFactory
- of(boolean, boolean) - Static method in class org.anchoranalysis.image.voxel.object.morphological.SelectDimensionsFactory
- of(Collection<ObjectMask>...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection with elements copied from existing collections
- of(Optional<ObjectCollection>...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection with elements copied from existing collections (if they exist)
- of(Stream<T>) - Static method in class org.anchoranalysis.core.functional.FunctionalList
-
Creates a list from a stream.
- of(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateDilation
- of(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
- of(CalculationResolver<FeatureInputSingleObject>, MorphologicalIterations, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
- of(SessionInput<FeatureInputSingleObject>, boolean) - Static method in class org.anchoranalysis.plugin.points.calculate.ellipsoid.CalculateEllipsoidLeastSquares
- of(BinaryVoxels<UnsignedByteBuffer>...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection with elements from the parameter-list of
BinaryVoxelsconverting the voxels in their entireity to an object-mask at the origin. - of(ObjectCollection...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection with elements copied from existing collections
- of(ObjectMask...) - Static method in class org.anchoranalysis.image.voxel.object.factory.ObjectCollectionFactory
-
Creates a new collection with elements from the parameter-list
- offset(int, int) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- offset(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
- offset(int, int) - Method in class org.anchoranalysis.spatial.Extent
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent
- offset(int, int, int) - Method in class org.anchoranalysis.spatial.Extent
-
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent
- offset(Point2i) - Method in class org.anchoranalysis.spatial.Extent
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent
- offset(Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- offset(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
-
Calculates a XYZ-offset of a point in a buffer whose dimensions are this extent
- offsetGlobal(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- offsetRelative(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- offsetSlice(Point3i) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- offsetSlice(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
-
Calculates a XY-offset of a point in a buffer whose dimensions are this extent
- OffsettedPointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
Like a
PointTwoDimensionalConsumerbut also has a buffer offset. - OffsettedScalarTwoDimensionalConsumer<E extends Exception> - Interface in org.anchoranalysis.spatial.point.consumer
-
Like a
ScalarTwoDimensionalConsumerbut accepts two coordinates of a point and an offset value. - ofResolved(CalculationResolver<FeatureInputSingleObject>, int, boolean) - Static method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological.CalculateErosion
- OMETiff - Class in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
-
Writes a stack to the filesystem as a OME-XML using the Bioformats library.
- OMETiff() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMETiff
- OMEXML - Class in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
-
Writes a stack to the filesystem as a OME-XML using the Bioformats library.
- OMEXML() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.OMEXML
- One - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects one specific channel from a set of stacks
- One() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
- oneOnly(String, String, boolean, boolean) - Static method in class org.anchoranalysis.bean.initializable.CheckMisconfigured
-
Checks that one of two properties is defined, but not both simultaneously (exclusive OR).
- OneStageGenerator<T> - Class in org.anchoranalysis.io.generator
- OneStageGenerator() - Constructor for class org.anchoranalysis.io.generator.OneStageGenerator
- ongoingTasksLessThan(int) - Method in class org.anchoranalysis.experiment.task.processor.ConcurrentJobMonitor
- onInit() - Method in class org.anchoranalysis.bean.NullParamsBean
-
As there's no parameters we expose a different method
- onInit() - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
- onInit(NullInitParams) - Method in class org.anchoranalysis.bean.NullParamsBean
- onInit(KeyValueParamsInitParams) - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
- onInit(FeatureInitParams) - Method in class org.anchoranalysis.feature.bean.Feature
-
Called after initialization.
- onInit(SharedFeaturesInitParams) - Method in class org.anchoranalysis.feature.bean.list.ReferencedFeatures
- onInit(SharedFeaturesInitParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
- onInit(ImageInitParams) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
- onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromInput
- onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
- onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
- onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
- onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
- onInit(ImageInitParams) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromInput
- onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
- onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
- onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
- onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
- onInit(MPPInitParams) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- onInit(PointsInitParams) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
- onInit(P) - Method in class org.anchoranalysis.bean.initializable.InitializableBean
-
Called after initialization.
- OnlyIf - Class in org.anchoranalysis.experiment.bean.log
-
Logs messages to a particular location ONLY if certain conditions are fulfilled.
- OnlyIf() - Constructor for class org.anchoranalysis.experiment.bean.log.OnlyIf
- open() - Method in interface org.anchoranalysis.core.progress.ProgressReporter
- open() - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
- open() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
- open() - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
- open() - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
- open(int, ProgressReporter) - Method in class org.anchoranalysis.io.bioformats.BioformatsOpenedRaster
- open(int, ProgressReporter) - Method in class org.anchoranalysis.plugin.io.multifile.MultiFileReaderOpenedRaster
- OpenCVWriter - Class in org.anchoranalysis.plugin.opencv.bean.writer
-
Writes a stack to the filesystem using OpenCV and a specified extension.
- OpenCVWriter() - Constructor for class org.anchoranalysis.plugin.opencv.bean.writer.OpenCVWriter
- openFile(Path) - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
- openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
- openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
- openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
- openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
- openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
- openFile(Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- openMarksFromFilePath(Path) - Static method in class org.anchoranalysis.test.experiment.TestLoaderMPP
- openMarksFromTestPath(String) - Method in class org.anchoranalysis.test.experiment.TestLoaderMPP
- openXmlAbsoluteFilePath(String) - Static method in class org.anchoranalysis.test.TestLoader
-
Opens a XML document - with an absolute path on the filesystem
- openXmlAbsoluteFilePath(Path) - Static method in class org.anchoranalysis.test.TestLoader
-
Opens a XML document - with an absolute path on the filesystem
- openXmlFromTestPath(String) - Method in class org.anchoranalysis.test.TestLoader
-
Opens a XML document - with a path relative to the test root
- OperationFailedException - Exception in org.anchoranalysis.core.exception
- OperationFailedException(String) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedException
- OperationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedException
- OperationFailedException(Throwable) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedException
- OperationFailedRuntimeException - Exception in org.anchoranalysis.core.exception
- OperationFailedRuntimeException(Exception) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedRuntimeException
- OperationFailedRuntimeException(String) - Constructor for exception org.anchoranalysis.core.exception.OperationFailedRuntimeException
- OperationMap<T> - Class in org.anchoranalysis.mpp.io.input
-
Stores objects as operations
- OperationMap() - Constructor for class org.anchoranalysis.mpp.io.input.OperationMap
- OptimizationContext - Class in org.anchoranalysis.mpp.segment.optimization
- OptimizationContext(String, EnergySchemeWithSharedFeatures, DualStack, TriggerTerminationCondition, InputOutputContext, RandomNumberGenerator, MarkWithIdentifierFactory) - Constructor for class org.anchoranalysis.mpp.segment.optimization.OptimizationContext
- OptimizationScheme<S,U> - Class in org.anchoranalysis.mpp.segment.bean.optimization
-
An optimization-scheme that uses kernels to make changes to state
- OptimizationScheme() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.OptimizationScheme
- OptimizationStep<S,T> - Class in org.anchoranalysis.mpp.segment.optimization.step
- OptimizationStep() - Constructor for class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- OptimizationStepLogReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- OptimizationStepLogReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
- OptimizationTerminatedEarlyException - Exception in org.anchoranalysis.mpp.segment.optimization
- OptimizationTerminatedEarlyException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.OptimizationTerminatedEarlyException
- OptionalBean - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that a field of a class can be set to null (omitted), otherwise by default a bean must always have a non-null value.
- OptionalFactory - Class in org.anchoranalysis.bean
-
Utility functions to create
Optionalfrom nullable providers or boolean flags. - OptionalNameValue<V> - Class in org.anchoranalysis.io.generator.combined
-
A simple container expressing a value and an associationed optional name.
- OptionalNameValue(Optional<String>, V) - Constructor for class org.anchoranalysis.io.generator.combined.OptionalNameValue
- OptionalOperationUnsupportedException - Exception in org.anchoranalysis.core.exception
- OptionalOperationUnsupportedException() - Constructor for exception org.anchoranalysis.core.exception.OptionalOperationUnsupportedException
- OptionalOperationUnsupportedException(Exception) - Constructor for exception org.anchoranalysis.core.exception.OptionalOperationUnsupportedException
- OptionalOperationUnsupportedException(String) - Constructor for exception org.anchoranalysis.core.exception.OptionalOperationUnsupportedException
- OptionalPointProposer - Interface in org.anchoranalysis.mpp.proposer
- OptionalUtilities - Class in org.anchoranalysis.core.functional
-
Additional utility functions for
Optionaland exceptions. - Or - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation or voxelwise on both masks, modifying {mask} with the result.
- Or - Class in org.anchoranalysis.plugin.image.bean.object.filter.combine
-
Applies multiples filter with logical OR i.e.
- Or() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Or
- Or() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.combine.Or
- order(String) - Method in interface org.anchoranalysis.core.index.bounded.OrderProvider
- OrderedFeatureList<T extends FeatureInput> - Interface in org.anchoranalysis.mpp.feature.addcriteria
- OrderedList - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
- OrderedList() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrderedList
- orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaEnergyPair
- orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaNever
- orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
- orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.ArbitraryPointCommon
- orderedListOfFeatures() - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
- orderedListOfFeatures() - Method in interface org.anchoranalysis.mpp.feature.addcriteria.OrderedFeatureList
-
A list of features used to determine the add-criteria, or null if irrelevant.
- orderedListOfFeatures() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
- orderedListOfFeatures() - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
- OrderedRadius - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
- OrderedRadius() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.OrderedRadius
- OrderProvider - Interface in org.anchoranalysis.core.index.bounded
- orElseGet(Optional<T>, CheckedSupplier<T, E>) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
-
Like
Optional.orElseGet(java.util.function.Supplier<? extends T>)but tolerates an exception in the supplier function, which is immediately thrown. - orFlat(Optional<T>...) - Static method in class org.anchoranalysis.core.functional.OptionalUtilities
-
The first optional if it's present, or the second, or the third etc.
- org.anchoranalysis.annotation - package org.anchoranalysis.annotation
-
Ground truth for an image in diverse forms.
- org.anchoranalysis.annotation.image - package org.anchoranalysis.annotation.image
-
Annotations that apply to an image as a whole.
- org.anchoranalysis.annotation.io - package org.anchoranalysis.annotation.io
-
Reading and writing annotations to the filesystem.
- org.anchoranalysis.annotation.io.assignment - package org.anchoranalysis.annotation.io.assignment
-
A pairing of objects from two collections (bipartite matching).
- org.anchoranalysis.annotation.io.assignment.generator - package org.anchoranalysis.annotation.io.assignment.generator
-
Generates output images to illustrate a
Assignmentbetween annotations. - org.anchoranalysis.annotation.io.bean - package org.anchoranalysis.annotation.io.bean
-
Beans related to reading / writing / specifying annotations.
- org.anchoranalysis.annotation.io.bean.comparer - package org.anchoranalysis.annotation.io.bean.comparer
-
What to compare an annotation (ground truth) against?
- org.anchoranalysis.annotation.io.image - package org.anchoranalysis.annotation.io.image
-
Reading and writing whole-image label annotations.
- org.anchoranalysis.annotation.io.image.findable - package org.anchoranalysis.annotation.io.image.findable
-
The outcome of searching for annotations or images on the file-system.
- org.anchoranalysis.annotation.io.mark - package org.anchoranalysis.annotation.io.mark
-
Reading and writing annotations basedupon marks to the file-system.
- org.anchoranalysis.annotation.mark - package org.anchoranalysis.annotation.mark
-
Annotations that use one or more marks to describe entities in an image.
- org.anchoranalysis.bean - package org.anchoranalysis.bean
-
Defining, loading, initializing Anchor Beans.
- org.anchoranalysis.bean.annotation - package org.anchoranalysis.bean.annotation
-
Annotations that decorate fields in an Anchor Bean.
- org.anchoranalysis.bean.define - package org.anchoranalysis.bean.define
-
Defineand related-classes. - org.anchoranalysis.bean.define.adder - package org.anchoranalysis.bean.define.adder
-
DefineAdderand related-classes. - org.anchoranalysis.bean.error - package org.anchoranalysis.bean.error
-
Exceptions that can occur executing generic operations on Anchor Beans.
- org.anchoranalysis.bean.initializable - package org.anchoranalysis.bean.initializable
-
Initializing beans with particular parameters, including recursively.
- org.anchoranalysis.bean.initializable.params - package org.anchoranalysis.bean.initializable.params
-
Some kinds of parameters used when initializing beans.
- org.anchoranalysis.bean.initializable.property - package org.anchoranalysis.bean.initializable.property
-
Performing initializion on particular properties in a bean.
- org.anchoranalysis.bean.permute - package org.anchoranalysis.bean.permute
-
Applying permutations to a bean's fields.
- org.anchoranalysis.bean.permute.property - package org.anchoranalysis.bean.permute.property
-
Applying permutations to the properties of a bean.
- org.anchoranalysis.bean.permute.setter - package org.anchoranalysis.bean.permute.setter
-
Setter used to impose a permutation on bean properties.
- org.anchoranalysis.bean.provider - package org.anchoranalysis.bean.provider
-
A means of creating / loading / referencing a bean from another bean or class.
- org.anchoranalysis.bean.shared - package org.anchoranalysis.bean.shared
-
Utility beans which have a generally broader use than a specific module.
- org.anchoranalysis.bean.shared.color - package org.anchoranalysis.bean.shared.color
-
Beans that specify colors.
- org.anchoranalysis.bean.shared.color.scheme - package org.anchoranalysis.bean.shared.color.scheme
-
Beans that create lists or indices of colors according to particular schemes.
- org.anchoranalysis.bean.shared.params - package org.anchoranalysis.bean.shared.params
-
Setting, referencing and initializing key-value parameters.
- org.anchoranalysis.bean.shared.params.keyvalue - package org.anchoranalysis.bean.shared.params.keyvalue
-
Referencing a particular
KeyValueParams. - org.anchoranalysis.bean.shared.path - package org.anchoranalysis.bean.shared.path
-
Defines a root path directory on the filesystem whre files are read / written.
- org.anchoranalysis.bean.shared.random - package org.anchoranalysis.bean.shared.random
-
Specifies a particular type of random-number generator.
- org.anchoranalysis.bean.shared.regex - package org.anchoranalysis.bean.shared.regex
-
Specifies regular-expressions.
- org.anchoranalysis.bean.shared.relation - package org.anchoranalysis.bean.shared.relation
-
Specifies a binary relation of some kind between scalars.
- org.anchoranalysis.bean.shared.relation.threshold - package org.anchoranalysis.bean.shared.relation.threshold
-
Specifies a unary relation to a *threshold* value.
- org.anchoranalysis.bean.store - package org.anchoranalysis.bean.store
-
Adding beans to collections.
- org.anchoranalysis.bean.xml - package org.anchoranalysis.bean.xml
-
Reading Beans from XML files.
- org.anchoranalysis.bean.xml.error - package org.anchoranalysis.bean.xml.error
-
Exceptions that can thrown when loading beans from XML.
- org.anchoranalysis.bean.xml.factory - package org.anchoranalysis.bean.xml.factory
-
Custom factories for loading beans in custom ways from XML.
- org.anchoranalysis.browser.launcher - package org.anchoranalysis.browser.launcher
-
Launching the anchor GUI interactive application from command-line.
- org.anchoranalysis.core.cache - package org.anchoranalysis.core.cache
-
Caching (memozing) calls to a method so an operation does not need to be repeated.
- org.anchoranalysis.core.color - package org.anchoranalysis.core.color
-
Specifying particular colors and groups of colors.
- org.anchoranalysis.core.concurrency - package org.anchoranalysis.core.concurrency
-
Specifying how many CPUs and GPUs can be allocated for some purpose.
- org.anchoranalysis.core.exception - package org.anchoranalysis.core.exception
-
Very general exceptions and base classes for exceptions with wide applicability.
- org.anchoranalysis.core.exception.combinable - package org.anchoranalysis.core.exception.combinable
-
Nested exceptions of similar type that can be combined together in a summary.
- org.anchoranalysis.core.exception.friendly - package org.anchoranalysis.core.exception.friendly
-
Particular types of exceptions that are guaranteed to have a text/form that gives user-friendly error descriptions.
- org.anchoranalysis.core.functional - package org.anchoranalysis.core.functional
-
Utilities and interfaces for applying functional-programming.
- org.anchoranalysis.core.functional.checked - package org.anchoranalysis.core.functional.checked
-
Versions of many functional-interfaces in
java.util.functionthat throw checked-exceptions. - org.anchoranalysis.core.graph - package org.anchoranalysis.core.graph
-
Data-structures for directed and undirected graphs, with or without an edge payload.
- org.anchoranalysis.core.identifier.getter - package org.anchoranalysis.core.identifier.getter
-
Data structures for adding a unique name (a String or integer identifier) to other entities.
- org.anchoranalysis.core.identifier.name - package org.anchoranalysis.core.identifier.name
-
Data structures for name (String) and value associations.
- org.anchoranalysis.core.identifier.provider - package org.anchoranalysis.core.identifier.provider
-
A collection of named-elements, a
NamedProvider, and related operations. - org.anchoranalysis.core.identifier.provider.store - package org.anchoranalysis.core.identifier.provider.store
-
Data structures like
NamedProviderwith supporting for adding new elements. - org.anchoranalysis.core.index - package org.anchoranalysis.core.index
-
Classes to support getting/setting/specifying unique-integers (indices) for elements.
- org.anchoranalysis.core.index.bounded - package org.anchoranalysis.core.index.bounded
-
A range of elements with indiced, bounded to lie between particular a minimum and maximum.
- org.anchoranalysis.core.index.bounded.bridge - package org.anchoranalysis.core.index.bounded.bridge
-
Exposes one type as a
BoundedIndexContainerof another type. - org.anchoranalysis.core.log - package org.anchoranalysis.core.log
-
Interfaces to log messages, both information and error messages.
- org.anchoranalysis.core.log.error - package org.anchoranalysis.core.log.error
-
Mechanism for reporting errors (exceptions/throwables) to the user.
- org.anchoranalysis.core.progress - package org.anchoranalysis.core.progress
-
Classes to allow for tracking the progress of a task that can be broken into smaller units, for reporting to the user.
- org.anchoranalysis.core.random - package org.anchoranalysis.core.random
-
Generating random numbers.
- org.anchoranalysis.core.serialize - package org.anchoranalysis.core.serialize
-
Utilities for serializing and deserializing objects.
- org.anchoranalysis.core.system - package org.anchoranalysis.core.system
-
Utilities for interacting with the operating system or computer system generally
- org.anchoranalysis.core.system.path - package org.anchoranalysis.core.system.path
-
Utilities for converting/manipulating file-paths.
- org.anchoranalysis.core.value - package org.anchoranalysis.core.value
-
Encapsulating values or sets of named-values.
- org.anchoranalysis.experiment - package org.anchoranalysis.experiment
-
Classes related to executing an experiment by calling jobs on inputs.
- org.anchoranalysis.experiment.bean - package org.anchoranalysis.experiment.bean
-
Beans related to executing an experiment by calling jobs on inputs.
- org.anchoranalysis.experiment.bean.identifier - package org.anchoranalysis.experiment.bean.identifier
-
Assigning unique names to experiments.
- org.anchoranalysis.experiment.bean.io - package org.anchoranalysis.experiment.bean.io
-
Generic experiments that handle input and output in structured ways.
- org.anchoranalysis.experiment.bean.log - package org.anchoranalysis.experiment.bean.log
-
Different approaches to where messages on the progress/status of an experiment are logged to.
- org.anchoranalysis.experiment.bean.processor - package org.anchoranalysis.experiment.bean.processor
-
How a task is executed on multiple inputs.
- org.anchoranalysis.experiment.bean.require - package org.anchoranalysis.experiment.bean.require
-
A test whether certain conditions on arguments to experiments are fulfilled.
- org.anchoranalysis.experiment.bean.task - package org.anchoranalysis.experiment.bean.task
-
Defines a task, which is a set of operations run on an input, that may or may not generate an output.
- org.anchoranalysis.experiment.io - package org.anchoranalysis.experiment.io
-
Interfaces for replacing attributes of an experiment: input, output, task etc.
- org.anchoranalysis.experiment.log - package org.anchoranalysis.experiment.log
-
Helpful classes for logging.
- org.anchoranalysis.experiment.task - package org.anchoranalysis.experiment.task
-
Non-bean classes related to a
Task. - org.anchoranalysis.experiment.task.processor - package org.anchoranalysis.experiment.task.processor
-
Non-bean classes related to
JobProcessor. - org.anchoranalysis.feature.bean - package org.anchoranalysis.feature.bean
-
Beans pertaining to feature-calculation.
- org.anchoranalysis.feature.bean.list - package org.anchoranalysis.feature.bean.list
-
A feature-list (custom list type for features) and associated providers.
- org.anchoranalysis.feature.bean.operator - package org.anchoranalysis.feature.bean.operator
-
Features that are sufficiently generic to work on any input-type.
- org.anchoranalysis.feature.bean.provider - package org.anchoranalysis.feature.bean.provider
-
Provider of a single feature.
- org.anchoranalysis.feature.bean.results - package org.anchoranalysis.feature.bean.results
-
Defines base class
FeatureResultstogether with some implementations. - org.anchoranalysis.feature.calculate - package org.anchoranalysis.feature.calculate
-
Sub-feature units of calculation that can be cached.
- org.anchoranalysis.feature.calculate.cache - package org.anchoranalysis.feature.calculate.cache
-
Classes to cache feature-results or parts of feature-results that occur repeatedly among features or across calculations of the same feature.
- org.anchoranalysis.feature.energy - package org.anchoranalysis.feature.energy
- org.anchoranalysis.feature.input - package org.anchoranalysis.feature.input
- org.anchoranalysis.feature.io.csv - package org.anchoranalysis.feature.io.csv
-
Writing feature calculation-results in CSV format.
- org.anchoranalysis.feature.io.name - package org.anchoranalysis.feature.io.name
-
Naming items in a weay that breaks down into multiple elements.
- org.anchoranalysis.feature.io.results - package org.anchoranalysis.feature.io.results
-
Writes feature-calculation results in different formats, also grouped results.
- org.anchoranalysis.feature.io.results.group - package org.anchoranalysis.feature.io.results.group
-
Various different outputs that can be written for the a grouped version of the results in
ResultsWriter. - org.anchoranalysis.feature.list - package org.anchoranalysis.feature.list
- org.anchoranalysis.feature.name - package org.anchoranalysis.feature.name
- org.anchoranalysis.feature.results - package org.anchoranalysis.feature.results
-
Results from one or more feature calculations.
- org.anchoranalysis.feature.session - package org.anchoranalysis.feature.session
- org.anchoranalysis.feature.session.cache - package org.anchoranalysis.feature.session.cache
- org.anchoranalysis.feature.session.cache.creator - package org.anchoranalysis.feature.session.cache.creator
- org.anchoranalysis.feature.session.cache.horizontal - package org.anchoranalysis.feature.session.cache.horizontal
- org.anchoranalysis.feature.session.calculator - package org.anchoranalysis.feature.session.calculator
- org.anchoranalysis.feature.session.calculator.cached - package org.anchoranalysis.feature.session.calculator.cached
- org.anchoranalysis.feature.session.strategy.child - package org.anchoranalysis.feature.session.strategy.child
- org.anchoranalysis.feature.session.strategy.replace - package org.anchoranalysis.feature.session.strategy.replace
- org.anchoranalysis.feature.session.strategy.replace.bind - package org.anchoranalysis.feature.session.strategy.replace.bind
- org.anchoranalysis.feature.shared - package org.anchoranalysis.feature.shared
-
Features shared for referencing among calculations.
- org.anchoranalysis.image.bean - package org.anchoranalysis.image.bean
-
Core (bean) classes for image processing.
- org.anchoranalysis.image.bean.channel.converter - package org.anchoranalysis.image.bean.channel.converter
-
Base classes for comparing a channel to another type.
- org.anchoranalysis.image.bean.interpolator - package org.anchoranalysis.image.bean.interpolator
-
Beans for specifying image interpolators.
- org.anchoranalysis.image.bean.nonbean.error - package org.anchoranalysis.image.bean.nonbean.error
-
Specific exception types that can be thrown in this module.
- org.anchoranalysis.image.bean.nonbean.init - package org.anchoranalysis.image.bean.nonbean.init
-
Initialization of image-related beans.
- org.anchoranalysis.image.bean.nonbean.segment - package org.anchoranalysis.image.bean.nonbean.segment
-
Non-bean classes relating to image-segmentation.
- org.anchoranalysis.image.bean.nonbean.spatial.arrange - package org.anchoranalysis.image.bean.nonbean.spatial.arrange
-
Non-beans to specify how to form a single-image by spatially combining other images.
- org.anchoranalysis.image.bean.object - package org.anchoranalysis.image.bean.object
-
Beans pertaining to
ObjectMaskand their collections. - org.anchoranalysis.image.bean.provider - package org.anchoranalysis.image.bean.provider
-
Base classes for providers of different core data entities related to images.
- org.anchoranalysis.image.bean.provider.stack - package org.anchoranalysis.image.bean.provider.stack
-
A provider of
Stacks. - org.anchoranalysis.image.bean.segment - package org.anchoranalysis.image.bean.segment
-
Base classes to perform image segmentation, transforming an image into another meaningful entity or entities.
- org.anchoranalysis.image.bean.segment.binary - package org.anchoranalysis.image.bean.segment.binary
-
Base classes to perform binary-segmentation.
- org.anchoranalysis.image.bean.segment.object - package org.anchoranalysis.image.bean.segment.object
-
Base classes to segment a channel into objects.
- org.anchoranalysis.image.bean.spatial - package org.anchoranalysis.image.bean.spatial
-
Beans to define entities or operate that consider Euclidian space.
- org.anchoranalysis.image.bean.spatial.arrange - package org.anchoranalysis.image.bean.spatial.arrange
-
Beans to specify how to form a single-image by spatially combining other images.
- org.anchoranalysis.image.bean.spatial.direction - package org.anchoranalysis.image.bean.spatial.direction
-
Beans to specify a direction.
- org.anchoranalysis.image.bean.threshold - package org.anchoranalysis.image.bean.threshold
-
Base classes for thresholding and calculating levels for thresholding.
- org.anchoranalysis.image.bean.threshold.relation - package org.anchoranalysis.image.bean.threshold.relation
-
Reusable relations to a threshold.
- org.anchoranalysis.image.bean.unitvalue.distance - package org.anchoranalysis.image.bean.unitvalue.distance
-
Converting quantities of distance between units.
- org.anchoranalysis.image.bean.unitvalue.extent - package org.anchoranalysis.image.bean.unitvalue.extent
-
Converting quantities of extent (area or volume) between units.
- org.anchoranalysis.image.bean.unitvalue.extent.area - package org.anchoranalysis.image.bean.unitvalue.extent.area
-
Converting quantities of area between units.
- org.anchoranalysis.image.bean.unitvalue.extent.volume - package org.anchoranalysis.image.bean.unitvalue.extent.volume
-
Converting quantities of volume between units.
- org.anchoranalysis.image.core.channel - package org.anchoranalysis.image.core.channel
-
The
Channelcore data-class and related operations and converters. - org.anchoranalysis.image.core.channel.convert - package org.anchoranalysis.image.core.channel.convert
-
Converts a channel to other data-types.
- org.anchoranalysis.image.core.channel.convert.attached - package org.anchoranalysis.image.core.channel.convert.attached
-
Converts a channel to another data-type based upon another object to which it is attached.
- org.anchoranalysis.image.core.channel.convert.attached.channel - package org.anchoranalysis.image.core.channel.convert.attached.channel
-
Converts a channel to another data-type based upon a
Channelto which it is attached. - org.anchoranalysis.image.core.channel.convert.attached.histogram - package org.anchoranalysis.image.core.channel.convert.attached.histogram
-
Converts a channel to another data-type based upon a
Histogramto which it is attached. - org.anchoranalysis.image.core.channel.factory - package org.anchoranalysis.image.core.channel.factory
-
Factory classes for creating
Channelfor various voxel data-types. - org.anchoranalysis.image.core.dimensions - package org.anchoranalysis.image.core.dimensions
-
Classes to describe the size of images or components of images both in voxels and physically.
- org.anchoranalysis.image.core.mask - package org.anchoranalysis.image.core.mask
-
An image with only two permissible states.
- org.anchoranalysis.image.core.mask.combine - package org.anchoranalysis.image.core.mask.combine
-
Binary operations involving voxelwise combination of
Mask. - org.anchoranalysis.image.core.merge - package org.anchoranalysis.image.core.merge
-
Merges two or more entities.
- org.anchoranalysis.image.core.object - package org.anchoranalysis.image.core.object
-
The key data entity
org.anchoranalysis.image.voxel.objectand related-classes and operations. - org.anchoranalysis.image.core.object.factory - package org.anchoranalysis.image.core.object.factory
-
Utilities to create
ObjectMaskandObjectCollection. - org.anchoranalysis.image.core.object.label - package org.anchoranalysis.image.core.object.label
-
Labelling elements (object-masks or similar) with unique successive integers in a channel.
- org.anchoranalysis.image.core.object.properties - package org.anchoranalysis.image.core.object.properties
- org.anchoranalysis.image.core.object.scale - package org.anchoranalysis.image.core.object.scale
-
Scaling object-collections, or lists of elements with object-representations.
- org.anchoranalysis.image.core.object.seed - package org.anchoranalysis.image.core.object.seed
- org.anchoranalysis.image.core.orientation - package org.anchoranalysis.image.core.orientation
-
Various methods to specify the orientation (general direction) of an entity.
- org.anchoranalysis.image.core.outline - package org.anchoranalysis.image.core.outline
-
Finds outline voxels i.e.
- org.anchoranalysis.image.core.outline.traverser - package org.anchoranalysis.image.core.outline.traverser
-
Performs a walk on every voxel on the outline of an object-mask.
- org.anchoranalysis.image.core.outline.traverser.path - package org.anchoranalysis.image.core.outline.traverser.path
- org.anchoranalysis.image.core.outline.traverser.visited - package org.anchoranalysis.image.core.outline.traverser.visited
- org.anchoranalysis.image.core.outline.traverser.visited.combine - package org.anchoranalysis.image.core.outline.traverser.visited.combine
- org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy - package org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy
- org.anchoranalysis.image.core.points - package org.anchoranalysis.image.core.points
- org.anchoranalysis.image.core.stack - package org.anchoranalysis.image.core.stack
- org.anchoranalysis.image.core.stack.bufferedimage - package org.anchoranalysis.image.core.stack.bufferedimage
- org.anchoranalysis.image.core.stack.rgb - package org.anchoranalysis.image.core.stack.rgb
- org.anchoranalysis.image.core.stack.wrap - package org.anchoranalysis.image.core.stack.wrap
- org.anchoranalysis.image.experiment.bean.task - package org.anchoranalysis.image.experiment.bean.task
- org.anchoranalysis.image.experiment.identifiers - package org.anchoranalysis.image.experiment.identifiers
- org.anchoranalysis.image.experiment.label - package org.anchoranalysis.image.experiment.label
- org.anchoranalysis.image.experiment.seed - package org.anchoranalysis.image.experiment.seed
- org.anchoranalysis.image.feature.bean - package org.anchoranalysis.image.feature.bean
-
Beans pertaining to feature definition and calculation.
- org.anchoranalysis.image.feature.bean.evaluator - package org.anchoranalysis.image.feature.bean.evaluator
-
Beans that define context (which feature, which energy-stack) for evaluating feature-inputs.
- org.anchoranalysis.image.feature.bean.object.collection - package org.anchoranalysis.image.feature.bean.object.collection
- org.anchoranalysis.image.feature.bean.object.pair - package org.anchoranalysis.image.feature.bean.object.pair
- org.anchoranalysis.image.feature.bean.object.single - package org.anchoranalysis.image.feature.bean.object.single
- org.anchoranalysis.image.feature.bean.physical - package org.anchoranalysis.image.feature.bean.physical
- org.anchoranalysis.image.feature.bean.physical.convert - package org.anchoranalysis.image.feature.bean.physical.convert
- org.anchoranalysis.image.feature.bean.score - package org.anchoranalysis.image.feature.bean.score
- org.anchoranalysis.image.feature.bean.stack - package org.anchoranalysis.image.feature.bean.stack
- org.anchoranalysis.image.feature.evaluator - package org.anchoranalysis.image.feature.evaluator
- org.anchoranalysis.image.feature.histogram - package org.anchoranalysis.image.feature.histogram
- org.anchoranalysis.image.feature.object.calculation - package org.anchoranalysis.image.feature.object.calculation
- org.anchoranalysis.image.feature.object.input - package org.anchoranalysis.image.feature.object.input
- org.anchoranalysis.image.feature.session - package org.anchoranalysis.image.feature.session
- org.anchoranalysis.image.feature.session.merged - package org.anchoranalysis.image.feature.session.merged
- org.anchoranalysis.image.feature.stack - package org.anchoranalysis.image.feature.stack
- org.anchoranalysis.image.voxel - package org.anchoranalysis.image.voxel
-
Data-structures to store and manipulate image raster-data or voxels.
- org.anchoranalysis.image.voxel.arithmetic - package org.anchoranalysis.image.voxel.arithmetic
-
Arithmetic operations for
Voxels. - org.anchoranalysis.image.voxel.assigner - package org.anchoranalysis.image.voxel.assigner
- org.anchoranalysis.image.voxel.binary - package org.anchoranalysis.image.voxel.binary
-
The
BinaryVoxelsclass and related operations. - org.anchoranalysis.image.voxel.binary.values - package org.anchoranalysis.image.voxel.binary.values
-
Defining on and off intensity-values to interpret an image in a binary way.
- org.anchoranalysis.image.voxel.buffer - package org.anchoranalysis.image.voxel.buffer
- org.anchoranalysis.image.voxel.buffer.max - package org.anchoranalysis.image.voxel.buffer.max
- org.anchoranalysis.image.voxel.buffer.mean - package org.anchoranalysis.image.voxel.buffer.mean
- org.anchoranalysis.image.voxel.buffer.primitive - package org.anchoranalysis.image.voxel.buffer.primitive
-
Conversion of both primitive data types and image structures between Anchor's data-structures and other representations.
- org.anchoranalysis.image.voxel.convert - package org.anchoranalysis.image.voxel.convert
-
Converting
Voxelsto different data-types. - org.anchoranalysis.image.voxel.convert.imglib2 - package org.anchoranalysis.image.voxel.convert.imglib2
-
Converts anchor data-structures to those used by ImgLib2.
- org.anchoranalysis.image.voxel.datatype - package org.anchoranalysis.image.voxel.datatype
- org.anchoranalysis.image.voxel.extracter - package org.anchoranalysis.image.voxel.extracter
- org.anchoranalysis.image.voxel.extracter.predicate - package org.anchoranalysis.image.voxel.extracter.predicate
- org.anchoranalysis.image.voxel.factory - package org.anchoranalysis.image.voxel.factory
- org.anchoranalysis.image.voxel.factory.sliceindex - package org.anchoranalysis.image.voxel.factory.sliceindex
- org.anchoranalysis.image.voxel.interpolator - package org.anchoranalysis.image.voxel.interpolator
-
Different interpolator methods to use when scaling voxels.
- org.anchoranalysis.image.voxel.iterator - package org.anchoranalysis.image.voxel.iterator
-
Utilities to iterate over voxel-locations in images and sub-regions of images.
- org.anchoranalysis.image.voxel.iterator.intersecting - package org.anchoranalysis.image.voxel.iterator.intersecting
-
Like
org.anchoranalysis.image.voxel.iteratorbut refers to iterators that operation over the intersecting regions of two entities. - org.anchoranalysis.image.voxel.iterator.neighbor - package org.anchoranalysis.image.voxel.iterator.neighbor
-
Iterating over a point's neighboring voxels.
- org.anchoranalysis.image.voxel.iterator.predicate - package org.anchoranalysis.image.voxel.iterator.predicate
-
Functional-interfaces for processing different combinations of points and buffers that return a boolean.
- org.anchoranalysis.image.voxel.iterator.predicate.buffer - package org.anchoranalysis.image.voxel.iterator.predicate.buffer
- org.anchoranalysis.image.voxel.iterator.process - package org.anchoranalysis.image.voxel.iterator.process
-
Functional-interfaces for processing different combinations of points and buffers that do not return a value.
- org.anchoranalysis.image.voxel.iterator.process.buffer - package org.anchoranalysis.image.voxel.iterator.process.buffer
-
Functional-interfaces for processing different combinations of points and raw buffers, but not
VoxelBuffer. - org.anchoranalysis.image.voxel.iterator.process.voxelbuffer - package org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
-
Functional-interfaces for processing different combinations of points and
VoxelBufferbut not raw buffers. - org.anchoranalysis.image.voxel.kernel - package org.anchoranalysis.image.voxel.kernel
- org.anchoranalysis.image.voxel.kernel.count - package org.anchoranalysis.image.voxel.kernel.count
- org.anchoranalysis.image.voxel.kernel.density - package org.anchoranalysis.image.voxel.kernel.density
- org.anchoranalysis.image.voxel.kernel.dilateerode - package org.anchoranalysis.image.voxel.kernel.dilateerode
- org.anchoranalysis.image.voxel.kernel.outline - package org.anchoranalysis.image.voxel.kernel.outline
- org.anchoranalysis.image.voxel.neighborhood - package org.anchoranalysis.image.voxel.neighborhood
- org.anchoranalysis.image.voxel.object - package org.anchoranalysis.image.voxel.object
- org.anchoranalysis.image.voxel.object.factory - package org.anchoranalysis.image.voxel.object.factory
- org.anchoranalysis.image.voxel.object.factory.unionfind - package org.anchoranalysis.image.voxel.object.factory.unionfind
-
Implements a union-find data-structure for connected-components.
- org.anchoranalysis.image.voxel.object.morphological - package org.anchoranalysis.image.voxel.object.morphological
- org.anchoranalysis.image.voxel.object.morphological.accept - package org.anchoranalysis.image.voxel.object.morphological.accept
- org.anchoranalysis.image.voxel.statistics - package org.anchoranalysis.image.voxel.statistics
-
Statistics about voxel intensities.
- org.anchoranalysis.image.voxel.thresholder - package org.anchoranalysis.image.voxel.thresholder
-
Thresholding operations on voxels.
- org.anchoranalysis.io.bioformats - package org.anchoranalysis.io.bioformats
-
Non-bean classes for filesystem I/O using Bioformats.
- org.anchoranalysis.io.bioformats.bean - package org.anchoranalysis.io.bioformats.bean
-
Beans for filesystem I/O using Bioformats.
- org.anchoranalysis.io.bioformats.bean.options - package org.anchoranalysis.io.bioformats.bean.options
-
User-specified options that can modify an opened-raster (e.g.
- org.anchoranalysis.io.bioformats.copyconvert - package org.anchoranalysis.io.bioformats.copyconvert
-
Converts the byte stream opened by Bioformats into channels of particular data-type.
- org.anchoranalysis.io.bioformats.copyconvert.tobyte - package org.anchoranalysis.io.bioformats.copyconvert.tobyte
-
Converts the byte stream opened by Bioformats into channels of
ByteBuffer. - org.anchoranalysis.io.bioformats.copyconvert.tofloat - package org.anchoranalysis.io.bioformats.copyconvert.tofloat
-
Converts the byte stream opened by Bioformats into channels of
FloatBuffer. - org.anchoranalysis.io.bioformats.copyconvert.toint - package org.anchoranalysis.io.bioformats.copyconvert.toint
-
Converts the byte stream opened by Bioformats into channels of
IntBuffer. - org.anchoranalysis.io.bioformats.copyconvert.toshort - package org.anchoranalysis.io.bioformats.copyconvert.toshort
-
Converts the byte stream opened by Bioformats into channels of
ShortBuffer. - org.anchoranalysis.io.generator - package org.anchoranalysis.io.generator
-
Base-classes and utilities for generators, which write different types of objects to the file system.
- org.anchoranalysis.io.generator.collection - package org.anchoranalysis.io.generator.collection
-
Outputting more than one element collectively using a generator.
- org.anchoranalysis.io.generator.combined - package org.anchoranalysis.io.generator.combined
-
Combining multiple generators into one.
- org.anchoranalysis.io.generator.sequence - package org.anchoranalysis.io.generator.sequence
-
Writing a sequence of elements using a generator.
- org.anchoranalysis.io.generator.sequence.pattern - package org.anchoranalysis.io.generator.sequence.pattern
- org.anchoranalysis.io.generator.serialized - package org.anchoranalysis.io.generator.serialized
-
Generators for writing serialized objects.
- org.anchoranalysis.io.generator.tabular - package org.anchoranalysis.io.generator.tabular
-
Generators for writing tabular data, including CSV.
- org.anchoranalysis.io.generator.text - package org.anchoranalysis.io.generator.text
-
Generators for writing textual data, including strings.
- org.anchoranalysis.io.generator.xml - package org.anchoranalysis.io.generator.xml
-
Generators for writing XML data.
- org.anchoranalysis.io.imagej.bean.stack.writer - package org.anchoranalysis.io.imagej.bean.stack.writer
-
Raster-writers that use ImageJ to write images to the filesystem.
- org.anchoranalysis.io.imagej.convert - package org.anchoranalysis.io.imagej.convert
-
Converts to and from ImageJ data-structures for images.
- org.anchoranalysis.io.manifest - package org.anchoranalysis.io.manifest
- org.anchoranalysis.io.manifest.deserializer - package org.anchoranalysis.io.manifest.deserializer
-
Classes to read manifests from the file-system.
- org.anchoranalysis.io.manifest.directory - package org.anchoranalysis.io.manifest.directory
-
Entities to indicate a directory in the manifest.
- org.anchoranalysis.io.manifest.directory.sequenced - package org.anchoranalysis.io.manifest.directory.sequenced
-
Classes related to a directory that has a particular sequence of outputted filenames.
- org.anchoranalysis.io.manifest.file - package org.anchoranalysis.io.manifest.file
-
Entities to indicate a file and its role in the manifest.
- org.anchoranalysis.io.manifest.finder - package org.anchoranalysis.io.manifest.finder
-
Methods to search through a manifest-file to find outputs matching certain conditions.
- org.anchoranalysis.io.manifest.finder.match - package org.anchoranalysis.io.manifest.finder.match
-
Predicates that are useful for matching against particular type of objects in finders.
- org.anchoranalysis.io.manifest.operationrecorder - package org.anchoranalysis.io.manifest.operationrecorder
-
Makes a record of each file/subdirectory written as output.
- org.anchoranalysis.io.manifest.sequencetype - package org.anchoranalysis.io.manifest.sequencetype
-
Predictable patterns of indexes as used in sets of outputted files.
- org.anchoranalysis.io.output.bean - package org.anchoranalysis.io.output.bean
-
Beans for the framework around writing files to the file-system.
- org.anchoranalysis.io.output.bean.enabled - package org.anchoranalysis.io.output.bean.enabled
-
Beans indicating whether a particular output is enabled or not.
- org.anchoranalysis.io.output.bean.path.prefixer - package org.anchoranalysis.io.output.bean.path.prefixer
-
Beans for generating paths for outputting files by adding a prefix, suffix etc.
- org.anchoranalysis.io.output.bean.rules - package org.anchoranalysis.io.output.bean.rules
-
Rules for determining if a particular output is enabled or not in a context of a hierarchy.
- org.anchoranalysis.io.output.enabled - package org.anchoranalysis.io.output.enabled
-
Non-beans pertaining to whether a particular output is enabled or not.
- org.anchoranalysis.io.output.enabled.multi - package org.anchoranalysis.io.output.enabled.multi
-
Non-beans that pertain to whether multiple-levels have outputs that are enabled or not.
- org.anchoranalysis.io.output.enabled.single - package org.anchoranalysis.io.output.enabled.single
-
Non-beans that pertain to whether a single level has outputs that are enabled or not.
- org.anchoranalysis.io.output.error - package org.anchoranalysis.io.output.error
-
Exceptions that may be thrown when writing files to the file-system.
- org.anchoranalysis.io.output.namestyle - package org.anchoranalysis.io.output.namestyle
-
Methods of naming a file with an index in the file-name.
- org.anchoranalysis.io.output.outputter - package org.anchoranalysis.io.output.outputter
-
Classes for outputting to particular directories.
- org.anchoranalysis.io.output.outputter.directory - package org.anchoranalysis.io.output.outputter.directory
-
BoundDirectoryand related classes. - org.anchoranalysis.io.output.path.prefixer - package org.anchoranalysis.io.output.path.prefixer
-
Non-beans for generating paths for outputting files by adding a prefix, suffix etc.
- org.anchoranalysis.io.output.recorded - package org.anchoranalysis.io.output.recorded
-
Classes for recording the output-names used as they are written / queried.
- org.anchoranalysis.io.output.writer - package org.anchoranalysis.io.output.writer
-
Allows a generators to write element(s) to the filesystem.
- org.anchoranalysis.io.output.xml - package org.anchoranalysis.io.output.xml
-
Outputting XML to the file-system.
- org.anchoranalysis.launcher - package org.anchoranalysis.launcher
- org.anchoranalysis.launcher.config - package org.anchoranalysis.launcher.config
- org.anchoranalysis.launcher.executor - package org.anchoranalysis.launcher.executor
- org.anchoranalysis.launcher.executor.selectparam - package org.anchoranalysis.launcher.executor.selectparam
- org.anchoranalysis.launcher.executor.selectparam.experiment - package org.anchoranalysis.launcher.executor.selectparam.experiment
- org.anchoranalysis.launcher.executor.selectparam.io - package org.anchoranalysis.launcher.executor.selectparam.io
- org.anchoranalysis.launcher.executor.selectparam.path - package org.anchoranalysis.launcher.executor.selectparam.path
- org.anchoranalysis.launcher.executor.selectparam.task - package org.anchoranalysis.launcher.executor.selectparam.task
- org.anchoranalysis.launcher.options - package org.anchoranalysis.launcher.options
-
A centralized location for all command-line options used by the launcher.
- org.anchoranalysis.launcher.options.outputs - package org.anchoranalysis.launcher.options.outputs
-
Adding/removing/changing the output(s) from the experiment via command-line-options.
- org.anchoranalysis.launcher.parser - package org.anchoranalysis.launcher.parser
- org.anchoranalysis.math.arithmetic - package org.anchoranalysis.math.arithmetic
-
Performing primitive type conversion, counting and summing.
- org.anchoranalysis.math.equation - package org.anchoranalysis.math.equation
- org.anchoranalysis.math.histogram - package org.anchoranalysis.math.histogram
-
The
Histogramcore data class and related operations. - org.anchoranalysis.math.moment - package org.anchoranalysis.math.moment
- org.anchoranalysis.math.optimization - package org.anchoranalysis.math.optimization
- org.anchoranalysis.math.relation - package org.anchoranalysis.math.relation
-
Different kinds of binary-relations.
- org.anchoranalysis.math.statistics - package org.anchoranalysis.math.statistics
- org.anchoranalysis.mpp.bean - package org.anchoranalysis.mpp.bean
- org.anchoranalysis.mpp.bean.anneal - package org.anchoranalysis.mpp.bean.anneal
- org.anchoranalysis.mpp.bean.bound - package org.anchoranalysis.mpp.bean.bound
- org.anchoranalysis.mpp.bean.init - package org.anchoranalysis.mpp.bean.init
- org.anchoranalysis.mpp.bean.mark - package org.anchoranalysis.mpp.bean.mark
- org.anchoranalysis.mpp.bean.mark.bounds - package org.anchoranalysis.mpp.bean.mark.bounds
- org.anchoranalysis.mpp.bean.mark.factory - package org.anchoranalysis.mpp.bean.mark.factory
- org.anchoranalysis.mpp.bean.points - package org.anchoranalysis.mpp.bean.points
- org.anchoranalysis.mpp.bean.points.fitter - package org.anchoranalysis.mpp.bean.points.fitter
- org.anchoranalysis.mpp.bean.points.updatable - package org.anchoranalysis.mpp.bean.points.updatable
- org.anchoranalysis.mpp.bean.proposer - package org.anchoranalysis.mpp.bean.proposer
- org.anchoranalysis.mpp.bean.proposer.radii - package org.anchoranalysis.mpp.bean.proposer.radii
- org.anchoranalysis.mpp.bean.provider - package org.anchoranalysis.mpp.bean.provider
- org.anchoranalysis.mpp.bean.regionmap - package org.anchoranalysis.mpp.bean.regionmap
- org.anchoranalysis.mpp.bound - package org.anchoranalysis.mpp.bound
- org.anchoranalysis.mpp.feature.addcriteria - package org.anchoranalysis.mpp.feature.addcriteria
- org.anchoranalysis.mpp.feature.bean.energy.element - package org.anchoranalysis.mpp.feature.bean.energy.element
- org.anchoranalysis.mpp.feature.bean.energy.scheme - package org.anchoranalysis.mpp.feature.bean.energy.scheme
- org.anchoranalysis.mpp.feature.bean.mark - package org.anchoranalysis.mpp.feature.bean.mark
- org.anchoranalysis.mpp.feature.bean.mark.collection - package org.anchoranalysis.mpp.feature.bean.mark.collection
- org.anchoranalysis.mpp.feature.energy - package org.anchoranalysis.mpp.feature.energy
- org.anchoranalysis.mpp.feature.energy.marks - package org.anchoranalysis.mpp.feature.energy.marks
- org.anchoranalysis.mpp.feature.energy.saved - package org.anchoranalysis.mpp.feature.energy.saved
- org.anchoranalysis.mpp.feature.energy.scheme - package org.anchoranalysis.mpp.feature.energy.scheme
- org.anchoranalysis.mpp.feature.error - package org.anchoranalysis.mpp.feature.error
- org.anchoranalysis.mpp.feature.input.memo - package org.anchoranalysis.mpp.feature.input.memo
- org.anchoranalysis.mpp.feature.mark - package org.anchoranalysis.mpp.feature.mark
- org.anchoranalysis.mpp.io.bean.input - package org.anchoranalysis.mpp.io.bean.input
- org.anchoranalysis.mpp.io.bean.report.feature - package org.anchoranalysis.mpp.io.bean.report.feature
- org.anchoranalysis.mpp.io.input - package org.anchoranalysis.mpp.io.input
- org.anchoranalysis.mpp.io.marks - package org.anchoranalysis.mpp.io.marks
- org.anchoranalysis.mpp.io.marks.generator - package org.anchoranalysis.mpp.io.marks.generator
- org.anchoranalysis.mpp.io.output - package org.anchoranalysis.mpp.io.output
- org.anchoranalysis.mpp.mark - package org.anchoranalysis.mpp.mark
- org.anchoranalysis.mpp.mark.conic - package org.anchoranalysis.mpp.mark.conic
- org.anchoranalysis.mpp.mark.points - package org.anchoranalysis.mpp.mark.points
- org.anchoranalysis.mpp.mark.set - package org.anchoranalysis.mpp.mark.set
- org.anchoranalysis.mpp.mark.voxelized - package org.anchoranalysis.mpp.mark.voxelized
- org.anchoranalysis.mpp.mark.voxelized.memo - package org.anchoranalysis.mpp.mark.voxelized.memo
- org.anchoranalysis.mpp.overlap - package org.anchoranalysis.mpp.overlap
- org.anchoranalysis.mpp.overlay - package org.anchoranalysis.mpp.overlay
- org.anchoranalysis.mpp.pair - package org.anchoranalysis.mpp.pair
- org.anchoranalysis.mpp.points - package org.anchoranalysis.mpp.points
- org.anchoranalysis.mpp.probmap - package org.anchoranalysis.mpp.probmap
- org.anchoranalysis.mpp.proposer - package org.anchoranalysis.mpp.proposer
- org.anchoranalysis.mpp.proposer.error - package org.anchoranalysis.mpp.proposer.error
- org.anchoranalysis.mpp.proposer.visualization - package org.anchoranalysis.mpp.proposer.visualization
- org.anchoranalysis.mpp.segment.bean - package org.anchoranalysis.mpp.segment.bean
-
Beans for segmentation algorithms related to marked-point-processes.
- org.anchoranalysis.mpp.segment.bean.define - package org.anchoranalysis.mpp.segment.bean.define
-
DefineOutputterand its sub-classes. - org.anchoranalysis.mpp.segment.bean.kernel - package org.anchoranalysis.mpp.segment.bean.kernel
-
Base classes for kernels that transition a configuration of marks (a
MarkCollection) into an altered version. - org.anchoranalysis.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.mpp.segment.bean.kernel.proposer
- org.anchoranalysis.mpp.segment.bean.optimization - package org.anchoranalysis.mpp.segment.bean.optimization
- org.anchoranalysis.mpp.segment.bean.optimization.feedback - package org.anchoranalysis.mpp.segment.bean.optimization.feedback
- org.anchoranalysis.mpp.segment.bean.optimization.termination - package org.anchoranalysis.mpp.segment.bean.optimization.termination
- org.anchoranalysis.mpp.segment.define - package org.anchoranalysis.mpp.segment.define
- org.anchoranalysis.mpp.segment.kernel - package org.anchoranalysis.mpp.segment.kernel
- org.anchoranalysis.mpp.segment.kernel.proposer - package org.anchoranalysis.mpp.segment.kernel.proposer
- org.anchoranalysis.mpp.segment.optimization - package org.anchoranalysis.mpp.segment.optimization
- org.anchoranalysis.mpp.segment.optimization.feedback - package org.anchoranalysis.mpp.segment.optimization.feedback
- org.anchoranalysis.mpp.segment.optimization.feedback.aggregate - package org.anchoranalysis.mpp.segment.optimization.feedback.aggregate
- org.anchoranalysis.mpp.segment.optimization.feedback.period - package org.anchoranalysis.mpp.segment.optimization.feedback.period
- org.anchoranalysis.mpp.segment.optimization.step - package org.anchoranalysis.mpp.segment.optimization.step
- org.anchoranalysis.mpp.segment.transformer - package org.anchoranalysis.mpp.segment.transformer
- org.anchoranalysis.mpp.voxel.partition - package org.anchoranalysis.mpp.voxel.partition
- org.anchoranalysis.mpp.voxel.partition.factory - package org.anchoranalysis.mpp.voxel.partition.factory
- org.anchoranalysis.overlay - package org.anchoranalysis.overlay
- org.anchoranalysis.overlay.bean - package org.anchoranalysis.overlay.bean
- org.anchoranalysis.overlay.collection - package org.anchoranalysis.overlay.collection
- org.anchoranalysis.overlay.identifier - package org.anchoranalysis.overlay.identifier
- org.anchoranalysis.overlay.object - package org.anchoranalysis.overlay.object
- org.anchoranalysis.overlay.object.scaled - package org.anchoranalysis.overlay.object.scaled
- org.anchoranalysis.overlay.writer - package org.anchoranalysis.overlay.writer
- org.anchoranalysis.plot - package org.anchoranalysis.plot
-
Plotting data on charts.
- org.anchoranalysis.plot.bean - package org.anchoranalysis.plot.bean
-
Beans for plotting.
- org.anchoranalysis.plot.bean.colorscheme - package org.anchoranalysis.plot.bean.colorscheme
-
Color schemes associated with plots.
- org.anchoranalysis.plot.index - package org.anchoranalysis.plot.index
-
Non-bean plot definitions.
- org.anchoranalysis.plugin.annotation.bean.aggregate - package org.anchoranalysis.plugin.annotation.bean.aggregate
-
Beans to combine two or more annotations.
- org.anchoranalysis.plugin.annotation.bean.comparer - package org.anchoranalysis.plugin.annotation.bean.comparer
-
Comparing the similarity of annotations from two images to each other.
- org.anchoranalysis.plugin.annotation.bean.comparison - package org.anchoranalysis.plugin.annotation.bean.comparison
- org.anchoranalysis.plugin.annotation.bean.comparison.assigner - package org.anchoranalysis.plugin.annotation.bean.comparison.assigner
-
Pairs annotations from two different sets, creating an assignment of some type.
- org.anchoranalysis.plugin.annotation.bean.file - package org.anchoranalysis.plugin.annotation.bean.file
-
FilesProviders for providing annotations. - org.anchoranalysis.plugin.annotation.bean.label - package org.anchoranalysis.plugin.annotation.bean.label
-
A label as used for annotating.
- org.anchoranalysis.plugin.annotation.bean.strategy - package org.anchoranalysis.plugin.annotation.bean.strategy
-
Strategies for how to annotate an image, such label per image etc.
- org.anchoranalysis.plugin.annotation.comparison - package org.anchoranalysis.plugin.annotation.comparison
-
Non-bean classes for comparing two sets of annotations.
- org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction - package org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction
-
Morphological grayscale-reconstruction algorithm.
- org.anchoranalysis.plugin.fiji.bean.channel.provider - package org.anchoranalysis.plugin.fiji.bean.channel.provider
-
Implementations of
ChannelProviderthat use FIJI. - org.anchoranalysis.plugin.fiji.bean.channel.provider.distance - package org.anchoranalysis.plugin.fiji.bean.channel.provider.distance
-
Euclidean Distance Transform implementations via FIJI.
- org.anchoranalysis.plugin.fiji.bean.define - package org.anchoranalysis.plugin.fiji.bean.define
-
Implementations of
DefineAdderBeanthat use FIJI. - org.anchoranalysis.plugin.fiji.bean.mask.provider - package org.anchoranalysis.plugin.fiji.bean.mask.provider
-
Implementations of
MaskProviderthat use FIJI. - org.anchoranalysis.plugin.fiji.bean.threshold - package org.anchoranalysis.plugin.fiji.bean.threshold
-
Implementations of
Thresholderthat use FIJI. - org.anchoranalysis.plugin.image.bean.blur - package org.anchoranalysis.plugin.image.bean.blur
- org.anchoranalysis.plugin.image.bean.box - package org.anchoranalysis.plugin.image.bean.box
-
Beans pertaining to bounding-boxes.
- org.anchoranalysis.plugin.image.bean.channel.convert - package org.anchoranalysis.plugin.image.bean.channel.convert
- org.anchoranalysis.plugin.image.bean.channel.convert.histogram - package org.anchoranalysis.plugin.image.bean.channel.convert.histogram
- org.anchoranalysis.plugin.image.bean.channel.provider - package org.anchoranalysis.plugin.image.bean.channel.provider
- org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic - package org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
- org.anchoranalysis.plugin.image.bean.channel.provider.assign - package org.anchoranalysis.plugin.image.bean.channel.provider.assign
- org.anchoranalysis.plugin.image.bean.channel.provider.convert - package org.anchoranalysis.plugin.image.bean.channel.provider.convert
- org.anchoranalysis.plugin.image.bean.channel.provider.gradient - package org.anchoranalysis.plugin.image.bean.channel.provider.gradient
- org.anchoranalysis.plugin.image.bean.channel.provider.intensity - package org.anchoranalysis.plugin.image.bean.channel.provider.intensity
- org.anchoranalysis.plugin.image.bean.channel.provider.mask - package org.anchoranalysis.plugin.image.bean.channel.provider.mask
- org.anchoranalysis.plugin.image.bean.channel.provider.object - package org.anchoranalysis.plugin.image.bean.channel.provider.object
- org.anchoranalysis.plugin.image.bean.channel.provider.score - package org.anchoranalysis.plugin.image.bean.channel.provider.score
- org.anchoranalysis.plugin.image.bean.channel.provider.slice - package org.anchoranalysis.plugin.image.bean.channel.provider.slice
- org.anchoranalysis.plugin.image.bean.color.provider - package org.anchoranalysis.plugin.image.bean.color.provider
- org.anchoranalysis.plugin.image.bean.dimensions.provider - package org.anchoranalysis.plugin.image.bean.dimensions.provider
- org.anchoranalysis.plugin.image.bean.histogram.provider - package org.anchoranalysis.plugin.image.bean.histogram.provider
- org.anchoranalysis.plugin.image.bean.histogram.threshold - package org.anchoranalysis.plugin.image.bean.histogram.threshold
- org.anchoranalysis.plugin.image.bean.mask.provider - package org.anchoranalysis.plugin.image.bean.mask.provider
- org.anchoranalysis.plugin.image.bean.mask.provider.combine - package org.anchoranalysis.plugin.image.bean.mask.provider.combine
- org.anchoranalysis.plugin.image.bean.mask.provider.convert - package org.anchoranalysis.plugin.image.bean.mask.provider.convert
- org.anchoranalysis.plugin.image.bean.mask.provider.dimensions - package org.anchoranalysis.plugin.image.bean.mask.provider.dimensions
- org.anchoranalysis.plugin.image.bean.mask.provider.morphological - package org.anchoranalysis.plugin.image.bean.mask.provider.morphological
- org.anchoranalysis.plugin.image.bean.mask.provider.predicate - package org.anchoranalysis.plugin.image.bean.mask.provider.predicate
- org.anchoranalysis.plugin.image.bean.mask.provider.resize - package org.anchoranalysis.plugin.image.bean.mask.provider.resize
- org.anchoranalysis.plugin.image.bean.mask.provider.segment - package org.anchoranalysis.plugin.image.bean.mask.provider.segment
- org.anchoranalysis.plugin.image.bean.mask.provider.slice - package org.anchoranalysis.plugin.image.bean.mask.provider.slice
- org.anchoranalysis.plugin.image.bean.object.filter - package org.anchoranalysis.plugin.image.bean.object.filter
- org.anchoranalysis.plugin.image.bean.object.filter.combine - package org.anchoranalysis.plugin.image.bean.object.filter.combine
- org.anchoranalysis.plugin.image.bean.object.filter.dependent - package org.anchoranalysis.plugin.image.bean.object.filter.dependent
- org.anchoranalysis.plugin.image.bean.object.filter.independent - package org.anchoranalysis.plugin.image.bean.object.filter.independent
- org.anchoranalysis.plugin.image.bean.object.match - package org.anchoranalysis.plugin.image.bean.object.match
- org.anchoranalysis.plugin.image.bean.object.provider - package org.anchoranalysis.plugin.image.bean.object.provider
- org.anchoranalysis.plugin.image.bean.object.provider.connected - package org.anchoranalysis.plugin.image.bean.object.provider.connected
- org.anchoranalysis.plugin.image.bean.object.provider.feature - package org.anchoranalysis.plugin.image.bean.object.provider.feature
- org.anchoranalysis.plugin.image.bean.object.provider.filter - package org.anchoranalysis.plugin.image.bean.object.provider.filter
- org.anchoranalysis.plugin.image.bean.object.provider.mask - package org.anchoranalysis.plugin.image.bean.object.provider.mask
- org.anchoranalysis.plugin.image.bean.object.provider.merge - package org.anchoranalysis.plugin.image.bean.object.provider.merge
- org.anchoranalysis.plugin.image.bean.object.provider.morphological - package org.anchoranalysis.plugin.image.bean.object.provider.morphological
- org.anchoranalysis.plugin.image.bean.object.provider.segment - package org.anchoranalysis.plugin.image.bean.object.provider.segment
- org.anchoranalysis.plugin.image.bean.object.provider.slice - package org.anchoranalysis.plugin.image.bean.object.provider.slice
- org.anchoranalysis.plugin.image.bean.object.provider.split - package org.anchoranalysis.plugin.image.bean.object.provider.split
- org.anchoranalysis.plugin.image.bean.object.segment.channel - package org.anchoranalysis.plugin.image.bean.object.segment.channel
- org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima
- org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction
- org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong - package org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong
- org.anchoranalysis.plugin.image.bean.object.segment.reduce - package org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
Strategies for reducing the number of elements with a list by merging/removing lower-confidence elements that overlap.
- org.anchoranalysis.plugin.image.bean.object.segment.stack - package org.anchoranalysis.plugin.image.bean.object.segment.stack
-
Instance-segmentation of a
Stack. - org.anchoranalysis.plugin.image.bean.params - package org.anchoranalysis.plugin.image.bean.params
- org.anchoranalysis.plugin.image.bean.scale - package org.anchoranalysis.plugin.image.bean.scale
- org.anchoranalysis.plugin.image.bean.segment.binary - package org.anchoranalysis.plugin.image.bean.segment.binary
- org.anchoranalysis.plugin.image.bean.stack.provider - package org.anchoranalysis.plugin.image.bean.stack.provider
- org.anchoranalysis.plugin.image.bean.stack.provider.color - package org.anchoranalysis.plugin.image.bean.stack.provider.color
- org.anchoranalysis.plugin.image.bean.stack.provider.plot - package org.anchoranalysis.plugin.image.bean.stack.provider.plot
- org.anchoranalysis.plugin.image.bean.thumbnail.object - package org.anchoranalysis.plugin.image.bean.thumbnail.object
- org.anchoranalysis.plugin.image.bean.thumbnail.stack - package org.anchoranalysis.plugin.image.bean.thumbnail.stack
- org.anchoranalysis.plugin.image.box - package org.anchoranalysis.plugin.image.box
-
Non-beans pertaining to bounding-boxes.
- org.anchoranalysis.plugin.image.channel - package org.anchoranalysis.plugin.image.channel
- org.anchoranalysis.plugin.image.feature.bean.dimensions - package org.anchoranalysis.plugin.image.feature.bean.dimensions
- org.anchoranalysis.plugin.image.feature.bean.histogram.statistic - package org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- org.anchoranalysis.plugin.image.feature.bean.histogram.threshold - package org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
- org.anchoranalysis.plugin.image.feature.bean.list.pair - package org.anchoranalysis.plugin.image.feature.bean.list.pair
- org.anchoranalysis.plugin.image.feature.bean.list.permute - package org.anchoranalysis.plugin.image.feature.bean.list.permute
- org.anchoranalysis.plugin.image.feature.bean.morphological - package org.anchoranalysis.plugin.image.feature.bean.morphological
- org.anchoranalysis.plugin.image.feature.bean.object.collection - package org.anchoranalysis.plugin.image.feature.bean.object.collection
- org.anchoranalysis.plugin.image.feature.bean.object.combine - package org.anchoranalysis.plugin.image.feature.bean.object.combine
- org.anchoranalysis.plugin.image.feature.bean.object.pair - package org.anchoranalysis.plugin.image.feature.bean.object.pair
- org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap - package org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
- org.anchoranalysis.plugin.image.feature.bean.object.pair.touching - package org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
- org.anchoranalysis.plugin.image.feature.bean.object.single - package org.anchoranalysis.plugin.image.feature.bean.object.single
- org.anchoranalysis.plugin.image.feature.bean.object.single.border - package org.anchoranalysis.plugin.image.feature.bean.object.single.border
- org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox - package org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox
- org.anchoranalysis.plugin.image.feature.bean.object.single.energy - package org.anchoranalysis.plugin.image.feature.bean.object.single.energy
- org.anchoranalysis.plugin.image.feature.bean.object.single.intensity - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
- org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient - package org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient
- org.anchoranalysis.plugin.image.feature.bean.object.single.moments - package org.anchoranalysis.plugin.image.feature.bean.object.single.moments
- org.anchoranalysis.plugin.image.feature.bean.object.single.morphological - package org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
- org.anchoranalysis.plugin.image.feature.bean.object.single.shape - package org.anchoranalysis.plugin.image.feature.bean.object.single.shape
- org.anchoranalysis.plugin.image.feature.bean.object.single.shared - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared
- org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting - package org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting
- org.anchoranalysis.plugin.image.feature.bean.object.single.slice - package org.anchoranalysis.plugin.image.feature.bean.object.single.slice
- org.anchoranalysis.plugin.image.feature.bean.object.single.surface - package org.anchoranalysis.plugin.image.feature.bean.object.single.surface
- org.anchoranalysis.plugin.image.feature.bean.physical - package org.anchoranalysis.plugin.image.feature.bean.physical
- org.anchoranalysis.plugin.image.feature.bean.score - package org.anchoranalysis.plugin.image.feature.bean.score
- org.anchoranalysis.plugin.image.feature.bean.shared - package org.anchoranalysis.plugin.image.feature.bean.shared
- org.anchoranalysis.plugin.image.feature.bean.shared.object - package org.anchoranalysis.plugin.image.feature.bean.shared.object
- org.anchoranalysis.plugin.image.feature.bean.stack.intensity - package org.anchoranalysis.plugin.image.feature.bean.stack.intensity
- org.anchoranalysis.plugin.image.feature.bean.stack.object - package org.anchoranalysis.plugin.image.feature.bean.stack.object
- org.anchoranalysis.plugin.image.feature.object - package org.anchoranalysis.plugin.image.feature.object
- org.anchoranalysis.plugin.image.feature.object.calculation.delegate - package org.anchoranalysis.plugin.image.feature.object.calculation.delegate
- org.anchoranalysis.plugin.image.feature.object.calculation.single - package org.anchoranalysis.plugin.image.feature.object.calculation.single
- org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological - package org.anchoranalysis.plugin.image.feature.object.calculation.single.morphological
- org.anchoranalysis.plugin.image.feature.stack.calculation - package org.anchoranalysis.plugin.image.feature.stack.calculation
- org.anchoranalysis.plugin.image.intensity - package org.anchoranalysis.plugin.image.intensity
- org.anchoranalysis.plugin.image.intensity.level - package org.anchoranalysis.plugin.image.intensity.level
- org.anchoranalysis.plugin.image.object - package org.anchoranalysis.plugin.image.object
- org.anchoranalysis.plugin.image.object.merge - package org.anchoranalysis.plugin.image.object.merge
- org.anchoranalysis.plugin.image.object.merge.condition - package org.anchoranalysis.plugin.image.object.merge.condition
- org.anchoranalysis.plugin.image.object.merge.priority - package org.anchoranalysis.plugin.image.object.merge.priority
- org.anchoranalysis.plugin.image.provider - package org.anchoranalysis.plugin.image.provider
- org.anchoranalysis.plugin.image.segment - package org.anchoranalysis.plugin.image.segment
- org.anchoranalysis.plugin.image.segment.thresholder.slice - package org.anchoranalysis.plugin.image.segment.thresholder.slice
- org.anchoranalysis.plugin.image.segment.watershed.encoding - package org.anchoranalysis.plugin.image.segment.watershed.encoding
- org.anchoranalysis.plugin.image.task.bean.feature - package org.anchoranalysis.plugin.image.task.bean.feature
-
Tasks pertaining to
Features. - org.anchoranalysis.plugin.image.task.bean.feature.source - package org.anchoranalysis.plugin.image.task.bean.feature.source
-
Source of rows in feature-tables with
FeatureSourceand derived classes. - org.anchoranalysis.plugin.image.task.bean.format - package org.anchoranalysis.plugin.image.task.bean.format
-
Tasks for converting image-formats.
- org.anchoranalysis.plugin.image.task.bean.format.convertstyle - package org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Different approaches for converting sets of channels (RGB, independently etc.) to another image format.
- org.anchoranalysis.plugin.image.task.bean.grouped - package org.anchoranalysis.plugin.image.task.bean.grouped
-
Tasks that involved stacks (usually each channel from an image) that are somehow grouped-together.
- org.anchoranalysis.plugin.image.task.bean.grouped.histogram - package org.anchoranalysis.plugin.image.task.bean.grouped.histogram
-
Task(s) to export histograms of intensity values.
- org.anchoranalysis.plugin.image.task.bean.grouped.raster - package org.anchoranalysis.plugin.image.task.bean.grouped.raster
-
Task(s) to calculate the mean of channels grouped together.
- org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels - package org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selecting a subset of a set of channels.
- org.anchoranalysis.plugin.image.task.bean.labeller - package org.anchoranalysis.plugin.image.task.bean.labeller
-
Associating labels with images.
- org.anchoranalysis.plugin.image.task.bean.scale - package org.anchoranalysis.plugin.image.task.bean.scale
- org.anchoranalysis.plugin.image.task.bean.segment - package org.anchoranalysis.plugin.image.task.bean.segment
-
Tasks to segment an image.
- org.anchoranalysis.plugin.image.task.bean.slice - package org.anchoranalysis.plugin.image.task.bean.slice
-
Tasks that process on one or more slices from a z-stack.
- org.anchoranalysis.plugin.image.task.channel - package org.anchoranalysis.plugin.image.task.channel
-
Non-bean classes pertaining to
Channels as used in tasks. - org.anchoranalysis.plugin.image.task.feature - package org.anchoranalysis.plugin.image.task.feature
-
Non-bean classes pertaining to
Features as used in tasks. - org.anchoranalysis.plugin.image.task.feature.calculator - package org.anchoranalysis.plugin.image.task.feature.calculator
-
Non-beans for calculating
Features. - org.anchoranalysis.plugin.image.task.grouped - package org.anchoranalysis.plugin.image.task.grouped
-
Non-bean classes about grouping channels or other inputs.
- org.anchoranalysis.plugin.image.task.labeller - package org.anchoranalysis.plugin.image.task.labeller
-
Non-bean classes about labelling images.
- org.anchoranalysis.plugin.image.task.segment - package org.anchoranalysis.plugin.image.task.segment
-
Non-bean classes for image-segmentation.
- org.anchoranalysis.plugin.image.task.slice - package org.anchoranalysis.plugin.image.task.slice
-
Non-bean cleasses pertaining to tasks that process on one or more slices from a z-stack.
- org.anchoranalysis.plugin.image.thumbnail - package org.anchoranalysis.plugin.image.thumbnail
-
Non-bean classes for thumbnail creation.
- org.anchoranalysis.plugin.imagej.bean.channel.provider - package org.anchoranalysis.plugin.imagej.bean.channel.provider
- org.anchoranalysis.plugin.imagej.bean.channel.provider.filter - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter
- org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
- org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank - package org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.rank
- org.anchoranalysis.plugin.imagej.bean.define - package org.anchoranalysis.plugin.imagej.bean.define
- org.anchoranalysis.plugin.imagej.bean.interpolator - package org.anchoranalysis.plugin.imagej.bean.interpolator
- org.anchoranalysis.plugin.imagej.bean.mask.provider - package org.anchoranalysis.plugin.imagej.bean.mask.provider
- org.anchoranalysis.plugin.imagej.bean.object.provider - package org.anchoranalysis.plugin.imagej.bean.object.provider
- org.anchoranalysis.plugin.imagej.bean.object.segment - package org.anchoranalysis.plugin.imagej.bean.object.segment
- org.anchoranalysis.plugin.imagej.bean.stack.provider - package org.anchoranalysis.plugin.imagej.bean.stack.provider
- org.anchoranalysis.plugin.imagej.bean.threshold - package org.anchoranalysis.plugin.imagej.bean.threshold
- org.anchoranalysis.plugin.imagej.channel.provider - package org.anchoranalysis.plugin.imagej.channel.provider
- org.anchoranalysis.plugin.imagej.mask - package org.anchoranalysis.plugin.imagej.mask
- org.anchoranalysis.plugin.io.bean.channel.map - package org.anchoranalysis.plugin.io.bean.channel.map
- org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod - package org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod
- org.anchoranalysis.plugin.io.bean.copyfilesmode.naming - package org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
- org.anchoranalysis.plugin.io.bean.descriptivename - package org.anchoranalysis.plugin.io.bean.descriptivename
- org.anchoranalysis.plugin.io.bean.descriptivename.patternspan - package org.anchoranalysis.plugin.io.bean.descriptivename.patternspan
- org.anchoranalysis.plugin.io.bean.experiment - package org.anchoranalysis.plugin.io.bean.experiment
- org.anchoranalysis.plugin.io.bean.filepath - package org.anchoranalysis.plugin.io.bean.filepath
- org.anchoranalysis.plugin.io.bean.filepath.prefixer - package org.anchoranalysis.plugin.io.bean.filepath.prefixer
- org.anchoranalysis.plugin.io.bean.groupfiles - package org.anchoranalysis.plugin.io.bean.groupfiles
- org.anchoranalysis.plugin.io.bean.groupfiles.check - package org.anchoranalysis.plugin.io.bean.groupfiles.check
- org.anchoranalysis.plugin.io.bean.groupfiles.parser - package org.anchoranalysis.plugin.io.bean.groupfiles.parser
- org.anchoranalysis.plugin.io.bean.input - package org.anchoranalysis.plugin.io.bean.input
- org.anchoranalysis.plugin.io.bean.input.channel - package org.anchoranalysis.plugin.io.bean.input.channel
- org.anchoranalysis.plugin.io.bean.input.files - package org.anchoranalysis.plugin.io.bean.input.files
- org.anchoranalysis.plugin.io.bean.input.files.provider - package org.anchoranalysis.plugin.io.bean.input.files.provider
- org.anchoranalysis.plugin.io.bean.input.filter - package org.anchoranalysis.plugin.io.bean.input.filter
- org.anchoranalysis.plugin.io.bean.input.manifest - package org.anchoranalysis.plugin.io.bean.input.manifest
- org.anchoranalysis.plugin.io.bean.input.stack - package org.anchoranalysis.plugin.io.bean.input.stack
- org.anchoranalysis.plugin.io.bean.path.derive - package org.anchoranalysis.plugin.io.bean.path.derive
- org.anchoranalysis.plugin.io.bean.provider.file - package org.anchoranalysis.plugin.io.bean.provider.file
- org.anchoranalysis.plugin.io.bean.stack.reader - package org.anchoranalysis.plugin.io.bean.stack.reader
- org.anchoranalysis.plugin.io.bean.stack.writer - package org.anchoranalysis.plugin.io.bean.stack.writer
- org.anchoranalysis.plugin.io.bean.stack.writer.bioformats - package org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
- org.anchoranalysis.plugin.io.bean.summarizer - package org.anchoranalysis.plugin.io.bean.summarizer
- org.anchoranalysis.plugin.io.bean.summarizer.image - package org.anchoranalysis.plugin.io.bean.summarizer.image
- org.anchoranalysis.plugin.io.bean.summarizer.input - package org.anchoranalysis.plugin.io.bean.summarizer.input
- org.anchoranalysis.plugin.io.bean.summarizer.path - package org.anchoranalysis.plugin.io.bean.summarizer.path
- org.anchoranalysis.plugin.io.bean.task - package org.anchoranalysis.plugin.io.bean.task
- org.anchoranalysis.plugin.io.input.filter - package org.anchoranalysis.plugin.io.input.filter
- org.anchoranalysis.plugin.io.input.path - package org.anchoranalysis.plugin.io.input.path
- org.anchoranalysis.plugin.io.manifest - package org.anchoranalysis.plugin.io.manifest
- org.anchoranalysis.plugin.io.multifile - package org.anchoranalysis.plugin.io.multifile
- org.anchoranalysis.plugin.io.multifile.buffer - package org.anchoranalysis.plugin.io.multifile.buffer
- org.anchoranalysis.plugin.io.summarizer - package org.anchoranalysis.plugin.io.summarizer
- org.anchoranalysis.plugin.io.xml - package org.anchoranalysis.plugin.io.xml
-
Reading and writing metadata XML.
- org.anchoranalysis.plugin.ml.bean.classifier - package org.anchoranalysis.plugin.ml.bean.classifier
- org.anchoranalysis.plugin.ml.bean.cluster - package org.anchoranalysis.plugin.ml.bean.cluster
-
Beans that perform clustering in some way.
- org.anchoranalysis.plugin.mpp.bean.addcriteria - package org.anchoranalysis.plugin.mpp.bean.addcriteria
- org.anchoranalysis.plugin.mpp.bean.bound - package org.anchoranalysis.plugin.mpp.bean.bound
- org.anchoranalysis.plugin.mpp.bean.check - package org.anchoranalysis.plugin.mpp.bean.check
- org.anchoranalysis.plugin.mpp.bean.define - package org.anchoranalysis.plugin.mpp.bean.define
- org.anchoranalysis.plugin.mpp.bean.distance - package org.anchoranalysis.plugin.mpp.bean.distance
- org.anchoranalysis.plugin.mpp.bean.object.provider - package org.anchoranalysis.plugin.mpp.bean.object.provider
- org.anchoranalysis.plugin.mpp.bean.outline - package org.anchoranalysis.plugin.mpp.bean.outline
- org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler - package org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
- org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection
- org.anchoranalysis.plugin.mpp.bean.proposer.mark.single - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
- org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection - package org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
- org.anchoranalysis.plugin.mpp.bean.proposer.merge - package org.anchoranalysis.plugin.mpp.bean.proposer.merge
- org.anchoranalysis.plugin.mpp.bean.proposer.orientation - package org.anchoranalysis.plugin.mpp.bean.proposer.orientation
- org.anchoranalysis.plugin.mpp.bean.proposer.points - package org.anchoranalysis.plugin.mpp.bean.proposer.points
- org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation - package org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
- org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline - package org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline
- org.anchoranalysis.plugin.mpp.bean.proposer.position - package org.anchoranalysis.plugin.mpp.bean.proposer.position
- org.anchoranalysis.plugin.mpp.bean.proposer.radii - package org.anchoranalysis.plugin.mpp.bean.proposer.radii
- org.anchoranalysis.plugin.mpp.bean.proposer.scalar - package org.anchoranalysis.plugin.mpp.bean.proposer.scalar
- org.anchoranalysis.plugin.mpp.bean.proposer.split - package org.anchoranalysis.plugin.mpp.bean.proposer.split
- org.anchoranalysis.plugin.mpp.bean.provider.collection - package org.anchoranalysis.plugin.mpp.bean.provider.collection
- org.anchoranalysis.plugin.mpp.bean.provider.single - package org.anchoranalysis.plugin.mpp.bean.provider.single
- org.anchoranalysis.plugin.mpp.bean.region - package org.anchoranalysis.plugin.mpp.bean.region
- org.anchoranalysis.plugin.mpp.bean.segment.binary - package org.anchoranalysis.plugin.mpp.bean.segment.binary
- org.anchoranalysis.plugin.mpp.bean.stack.provider - package org.anchoranalysis.plugin.mpp.bean.stack.provider
- org.anchoranalysis.plugin.mpp.experiment.bean - package org.anchoranalysis.plugin.mpp.experiment.bean
- org.anchoranalysis.plugin.mpp.experiment.bean.define - package org.anchoranalysis.plugin.mpp.experiment.bean.define
- org.anchoranalysis.plugin.mpp.experiment.bean.feature.report - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
- org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task
- org.anchoranalysis.plugin.mpp.experiment.bean.feature.source - package org.anchoranalysis.plugin.mpp.experiment.bean.feature.source
- org.anchoranalysis.plugin.mpp.experiment.bean.objects - package org.anchoranalysis.plugin.mpp.experiment.bean.objects
- org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition - package org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
- org.anchoranalysis.plugin.mpp.experiment.bean.output - package org.anchoranalysis.plugin.mpp.experiment.bean.output
- org.anchoranalysis.plugin.mpp.experiment.bean.segment - package org.anchoranalysis.plugin.mpp.experiment.bean.segment
- org.anchoranalysis.plugin.mpp.experiment.objects - package org.anchoranalysis.plugin.mpp.experiment.objects
- org.anchoranalysis.plugin.mpp.experiment.objects.csv - package org.anchoranalysis.plugin.mpp.experiment.objects.csv
- org.anchoranalysis.plugin.mpp.feature.bean.mark.collection - package org.anchoranalysis.plugin.mpp.feature.bean.mark.collection
- org.anchoranalysis.plugin.mpp.feature.bean.mark.direction - package org.anchoranalysis.plugin.mpp.feature.bean.mark.direction
- org.anchoranalysis.plugin.mpp.feature.bean.mark.radii - package org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
- org.anchoranalysis.plugin.mpp.feature.bean.mark.region - package org.anchoranalysis.plugin.mpp.feature.bean.mark.region
- org.anchoranalysis.plugin.mpp.feature.bean.memo.all - package org.anchoranalysis.plugin.mpp.feature.bean.memo.all
- org.anchoranalysis.plugin.mpp.feature.bean.memo.ind - package org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
- org.anchoranalysis.plugin.mpp.feature.bean.memo.pair - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair
- org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance
- org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap - package org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
- org.anchoranalysis.plugin.mpp.feature.bean.unit - package org.anchoranalysis.plugin.mpp.feature.bean.unit
- org.anchoranalysis.plugin.mpp.feature.overlap - package org.anchoranalysis.plugin.mpp.feature.overlap
- org.anchoranalysis.plugin.mpp.segment - package org.anchoranalysis.plugin.mpp.segment
- org.anchoranalysis.plugin.mpp.segment.bean.annealing - package org.anchoranalysis.plugin.mpp.segment.bean.annealing
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized
- org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer - package org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer
- org.anchoranalysis.plugin.mpp.segment.bean.marks - package org.anchoranalysis.plugin.mpp.segment.bean.marks
- org.anchoranalysis.plugin.mpp.segment.bean.marks.dual - package org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
- org.anchoranalysis.plugin.mpp.segment.bean.marks.partition - package org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
- org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized - package org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
- org.anchoranalysis.plugin.mpp.segment.bean.marks.weight - package org.anchoranalysis.plugin.mpp.segment.bean.marks.weight
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
- org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination - package org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
- org.anchoranalysis.plugin.mpp.segment.kernel.assigner - package org.anchoranalysis.plugin.mpp.segment.kernel.assigner
- org.anchoranalysis.plugin.mpp.segment.kernel.updater - package org.anchoranalysis.plugin.mpp.segment.kernel.updater
- org.anchoranalysis.plugin.mpp.segment.optimization - package org.anchoranalysis.plugin.mpp.segment.optimization
- org.anchoranalysis.plugin.opencv - package org.anchoranalysis.plugin.opencv
- org.anchoranalysis.plugin.opencv.bean.feature - package org.anchoranalysis.plugin.opencv.bean.feature
- org.anchoranalysis.plugin.opencv.bean.object.segment.stack - package org.anchoranalysis.plugin.opencv.bean.object.segment.stack
- org.anchoranalysis.plugin.opencv.bean.stack.provider.color - package org.anchoranalysis.plugin.opencv.bean.stack.provider.color
- org.anchoranalysis.plugin.opencv.bean.writer - package org.anchoranalysis.plugin.opencv.bean.writer
-
Implementations of
StackWriterand any other types of writers that use OpenCV. - org.anchoranalysis.plugin.opencv.convert - package org.anchoranalysis.plugin.opencv.convert
- org.anchoranalysis.plugin.operator.feature.bean - package org.anchoranalysis.plugin.operator.feature.bean
- org.anchoranalysis.plugin.operator.feature.bean.arithmetic - package org.anchoranalysis.plugin.operator.feature.bean.arithmetic
- org.anchoranalysis.plugin.operator.feature.bean.conditional - package org.anchoranalysis.plugin.operator.feature.bean.conditional
- org.anchoranalysis.plugin.operator.feature.bean.list - package org.anchoranalysis.plugin.operator.feature.bean.list
- org.anchoranalysis.plugin.operator.feature.bean.range - package org.anchoranalysis.plugin.operator.feature.bean.range
- org.anchoranalysis.plugin.operator.feature.bean.range.feature - package org.anchoranalysis.plugin.operator.feature.bean.range.feature
- org.anchoranalysis.plugin.operator.feature.bean.replace - package org.anchoranalysis.plugin.operator.feature.bean.replace
- org.anchoranalysis.plugin.operator.feature.bean.score - package org.anchoranalysis.plugin.operator.feature.bean.score
- org.anchoranalysis.plugin.operator.feature.physical - package org.anchoranalysis.plugin.operator.feature.physical
- org.anchoranalysis.plugin.operator.feature.score - package org.anchoranalysis.plugin.operator.feature.score
- org.anchoranalysis.plugin.points.bean.contour - package org.anchoranalysis.plugin.points.bean.contour
- org.anchoranalysis.plugin.points.bean.feature.object.conic - package org.anchoranalysis.plugin.points.bean.feature.object.conic
- org.anchoranalysis.plugin.points.bean.fitter - package org.anchoranalysis.plugin.points.bean.fitter
- org.anchoranalysis.plugin.points.bean.mark.proposer.single - package org.anchoranalysis.plugin.points.bean.mark.proposer.single
- org.anchoranalysis.plugin.points.bean.mark.provider.collection - package org.anchoranalysis.plugin.points.bean.mark.provider.collection
- org.anchoranalysis.plugin.points.bean.mark.provider.single - package org.anchoranalysis.plugin.points.bean.mark.provider.single
- org.anchoranalysis.plugin.points.bean.mask.provider - package org.anchoranalysis.plugin.points.bean.mask.provider
- org.anchoranalysis.plugin.points.bean.provider.object - package org.anchoranalysis.plugin.points.bean.provider.object
- org.anchoranalysis.plugin.points.calculate - package org.anchoranalysis.plugin.points.calculate
- org.anchoranalysis.plugin.points.calculate.ellipse - package org.anchoranalysis.plugin.points.calculate.ellipse
- org.anchoranalysis.plugin.points.calculate.ellipsoid - package org.anchoranalysis.plugin.points.calculate.ellipsoid
- org.anchoranalysis.plugin.points.contour - package org.anchoranalysis.plugin.points.contour
- org.anchoranalysis.plugin.points.convexhull - package org.anchoranalysis.plugin.points.convexhull
- org.anchoranalysis.plugin.quick.bean.experiment - package org.anchoranalysis.plugin.quick.bean.experiment
- org.anchoranalysis.plugin.quick.bean.file.path.derive - package org.anchoranalysis.plugin.quick.bean.file.path.derive
- org.anchoranalysis.plugin.quick.bean.input - package org.anchoranalysis.plugin.quick.bean.input
- org.anchoranalysis.plugin.quick.bean.input.filepathappend - package org.anchoranalysis.plugin.quick.bean.input.filepathappend
- org.anchoranalysis.plugin.quick.bean.structure - package org.anchoranalysis.plugin.quick.bean.structure
- org.anchoranalysis.spatial - package org.anchoranalysis.spatial
- org.anchoranalysis.spatial.axis - package org.anchoranalysis.spatial.axis
-
Identifying the three standard axes in 3D cartesian coordinates.
- org.anchoranalysis.spatial.box - package org.anchoranalysis.spatial.box
-
Axis-aligned bounding-boxes and related operations.
- org.anchoranalysis.spatial.point - package org.anchoranalysis.spatial.point
-
A cartesian-coordinate, across varying primitive types, in 2D and 3D space.
- org.anchoranalysis.spatial.point.consumer - package org.anchoranalysis.spatial.point.consumer
-
Functional interfaces that accept cartesian coordinate points specified in different ways.
- org.anchoranalysis.spatial.rotation - package org.anchoranalysis.spatial.rotation
-
A matrix to apply a rotation to a point.
- org.anchoranalysis.spatial.rotation.factory - package org.anchoranalysis.spatial.rotation.factory
-
Creates
RotationMatrixin varying ways. - org.anchoranalysis.spatial.rtree - package org.anchoranalysis.spatial.rtree
-
R-Tree data structure and related operations.
- org.anchoranalysis.spatial.scale - package org.anchoranalysis.spatial.scale
-
How to much to scale an entity in Cartesian space by.
- org.anchoranalysis.test - package org.anchoranalysis.test
-
Testing utilities and fixtures with no greater downstream dependency than anchor-core.
- org.anchoranalysis.test.experiment - package org.anchoranalysis.test.experiment
-
Testing utilities and fixtures with no greater downstream dependency than anchor-experiment or anchor-mpp or anchor-mpp-io.
- org.anchoranalysis.test.experiment.launcher - package org.anchoranalysis.test.experiment.launcher
-
Launches an anchor binary from a shell and runs an experiment.
- org.anchoranalysis.test.feature - package org.anchoranalysis.test.feature
-
Testing utilities and fixtures with no greater downstream dependency than anchor-feature.
- org.anchoranalysis.test.feature.plugins - package org.anchoranalysis.test.feature.plugins
-
Testing utilities and fixtures with no greater downstream dependency than anchor-image-feature or anchor-mpp.
- org.anchoranalysis.test.feature.plugins.mockfeature - package org.anchoranalysis.test.feature.plugins.mockfeature
-
A mocked feature internally using a feature-calculation.
- org.anchoranalysis.test.feature.plugins.objects - package org.anchoranalysis.test.feature.plugins.objects
-
Fixtures for creating object-masks and related feature-inputs.
- OrientableBounds - Class in org.anchoranalysis.mpp.bean.bound
- OrientableBounds() - Constructor for class org.anchoranalysis.mpp.bean.bound.OrientableBounds
- Orientation - Class in org.anchoranalysis.image.core.orientation
- Orientation() - Constructor for class org.anchoranalysis.image.core.orientation.Orientation
- Orientation2D - Class in org.anchoranalysis.image.core.orientation
- Orientation2D() - Constructor for class org.anchoranalysis.image.core.orientation.Orientation2D
- Orientation2D(double) - Constructor for class org.anchoranalysis.image.core.orientation.Orientation2D
- Orientation3DEulerAngles - Class in org.anchoranalysis.image.core.orientation
- Orientation3DEulerAngles() - Constructor for class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
- Orientation3DEulerAngles(double, double, double) - Constructor for class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
- OrientationAndRadiiProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
-
Proposes both an orientation and radii for a
ConicBase - OrientationAndRadiiProposer(RadiiProposer, OrientationProposer) - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
- OrientationAxisAngle - Class in org.anchoranalysis.image.core.orientation
-
An orientation in axis-angle representation.
- OrientationAxisAngle(Vector3d, double) - Constructor for class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
- OrientationIdentity - Class in org.anchoranalysis.image.core.orientation
- OrientationIdentity(int) - Constructor for class org.anchoranalysis.image.core.orientation.OrientationIdentity
- OrientationProposer - Class in org.anchoranalysis.mpp.bean.proposer
- OrientationProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.OrientationProposer
- OrientationRotationMatrix - Class in org.anchoranalysis.image.core.orientation
- OrientationRotationMatrix() - Constructor for class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
- OrientationRotationMatrix(RotationMatrix) - Constructor for class org.anchoranalysis.image.core.orientation.OrientationRotationMatrix
- otherVertex(V) - Method in class org.anchoranalysis.core.graph.TypedEdge
-
The other vertex on the edge
- Otsu - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Performs auto-thresholding using Otsu's method.
- Otsu() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Otsu
- OtsuWeighted - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Similar to Otsu, but weighs the variances differently of background and foreground
- OtsuWeighted() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
- OtsuWeighted(double, double) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
- outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
-
Provides a prefix which can be prepended to all output files.
- outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
- outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
- outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
- outFilePrefix(NamedPath, String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
- outFilePrefixAvoidResolve(NamedPath, String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
-
Provides a prefix which can be prepended to all output files.
- outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
- outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
-
Determines the out-file prefix from a path
- outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
- outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.FromDescriptiveName
- outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
- outFilePrefixFromPath(NamedPath, Path) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.PathRegEx
- outgoingEdgesFor(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
All outgoing edges for a given vertex.
- outline(Mask, int, boolean, boolean) - Static method in class org.anchoranalysis.image.core.outline.FindOutline
-
Creates an outline of depth 1 from a mask
- outline(ObjectMask, int, boolean, boolean) - Static method in class org.anchoranalysis.image.core.outline.FindOutline
-
Creates outline from an object
- Outline - Class in org.anchoranalysis.plugin.image.bean.mask.provider.morphological
-
Always creates a new mask for the result (no need to duplicate input)
- Outline() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
- outlineGuess3D(Mask, int, boolean, boolean) - Static method in class org.anchoranalysis.image.core.outline.FindOutline
-
Finds the outline of a mask, guessing whether to do this in 2D or 3D depending on if the mask has 3-dimensions
- OutlineKernel3 - Class in org.anchoranalysis.image.voxel.kernel.outline
- OutlineKernel3(BinaryValuesByte, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3
- OutlineKernel3(BinaryValuesByte, OutlineKernelParameters) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3
- OutlineKernel3Base - Class in org.anchoranalysis.image.voxel.kernel.outline
- OutlineKernel3Base(BinaryValuesByte, OutlineKernelParameters) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3Base
- OutlineKernel3NeighborMatchValue - Class in org.anchoranalysis.image.voxel.kernel.outline
- OutlineKernel3NeighborMatchValue(ObjectMask, BinaryVoxels<UnsignedByteBuffer>, OutlineKernelParameters) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernel3NeighborMatchValue
- OutlineKernelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single
- OutlineKernelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
- OutlineKernelParameters - Class in org.anchoranalysis.image.voxel.kernel.outline
- OutlineKernelParameters(boolean, boolean, boolean) - Constructor for class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
- OutlinePixelsRetriever - Class in org.anchoranalysis.plugin.mpp.bean.outline
- OutlinePixelsRetriever() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.OutlinePixelsRetriever
- OutlinePreserveRelativeSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object
-
Create a thumbnail by drawing an outline of an object at a particular-scale, and placing it centered in a window of a certain size.
- OutlinePreserveRelativeSize() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
- OutlineTraverser - Class in org.anchoranalysis.image.core.outline.traverser
- OutlineTraverser(ObjectMask, ConsiderVisit, boolean, boolean) - Constructor for class org.anchoranalysis.image.core.outline.traverser.OutlineTraverser
- output(String, boolean) - Method in class org.anchoranalysis.io.generator.collection.NamedProviderOutputter
-
Outputs the entities using a particular output-name.
- OUTPUT_DEFAULT_NON_AGGREGATED - Static variable in class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
-
If not otherwise specified, the output name for a non-aggregated CSV of the results.
- OUTPUT_NAME_MANIFEST - Static variable in class org.anchoranalysis.experiment.bean.io.OutputExperiment
- OUTPUT_NAME_MANIFEST - Static variable in class org.anchoranalysis.experiment.bean.task.Task
- OUTPUT_RESULTS - Static variable in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
- OUTPUT_SUMMARY_CSV - Static variable in class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
- OUTPUT_THUMBNAILS - Static variable in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
- outputAfterAllTasksAreExecuted(Outputter) - Method in interface org.anchoranalysis.mpp.segment.bean.ExperimentState
- outputAfterAllTasksAreExecuted(Outputter) - Method in class org.anchoranalysis.plugin.mpp.segment.SgmnMPPState
- outputBeforeAnyTasksAreExecuted(Outputter) - Method in interface org.anchoranalysis.mpp.segment.bean.ExperimentState
- outputBeforeAnyTasksAreExecuted(Outputter) - Method in class org.anchoranalysis.plugin.mpp.segment.SgmnMPPState
- OutputDirectoryAlreadyExistsException - Exception in org.anchoranalysis.io.output.error
-
When an output-directory already exists.
- OutputDirectoryAlreadyExistsException(String) - Constructor for exception org.anchoranalysis.io.output.error.OutputDirectoryAlreadyExistsException
- OutputEnabled - Class in org.anchoranalysis.io.output.bean.enabled
-
Whether a particular output, identified by a textual name, is enabled or not.
- OutputEnabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.OutputEnabled
- OutputEnabledDelta - Class in org.anchoranalysis.io.output.recorded
-
Additional output-names to enable or disable from an existing set of output-enabled rules.
- OutputEnabledDelta() - Constructor for class org.anchoranalysis.io.output.recorded.OutputEnabledDelta
- OutputEnabledMutable - Class in org.anchoranalysis.io.output.enabled
-
A specific set of first-level outputs are enabled, to which more can be added.
- OutputEnabledMutable(String...) - Constructor for class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
-
Creates with one or more enabled outputs.
- OutputEnabledMutable(SingleLevelOutputEnabled, String...) - Constructor for class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
-
Creates with one or more enabled outputs.
- OutputEnabledRules - Class in org.anchoranalysis.io.output.bean.rules
-
Bean that specifies an implementation of
MultiLevelOutputEnabled. - OutputEnabledRules() - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnabledRules
- OutputEnableRulesSpecify - Class in org.anchoranalysis.io.output.bean.rules
-
Base class for an
OutputEnabledRulesthat specifies particular output-names for first and second levels. - OutputEnableRulesSpecify() - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
- OutputEnableRulesSpecify(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
-
Create with a specific set of first-level output names.
- OutputExperiment - Class in org.anchoranalysis.experiment.bean.io
-
An experiment that uses a
OutputManagerto specify the outputting of results. - OutputExperiment() - Constructor for class org.anchoranalysis.experiment.bean.io.OutputExperiment
- OutputFactory - Class in org.anchoranalysis.launcher.executor.selectparam.io
-
SelectParam<Path>factory for outputs. - outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
- outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.IntegerSuffixOutputNameStyle
- outputFormatString() - Method in class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
- outputGroupedData(ConsistentChannelChecker, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName
-
Outputs the "grouped" data to the filesystem
- outputHeaderToWriter(PrintWriter) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- outputHeaderToWriter(PrintWriter, String) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
- OutputManager - Class in org.anchoranalysis.io.output.bean
-
Responsible for making decisions on where output goes and what form it takes.
- OutputManager() - Constructor for class org.anchoranalysis.io.output.bean.OutputManager
- outputName(String) - Static method in class org.anchoranalysis.io.manifest.finder.match.FileMatch
-
Match a file whose output-name matches a specific value.
- outputNames() - Method in class org.anchoranalysis.feature.io.results.ResultsWriterMetadata
-
Names for any outputs produced by
ResultsWriter. - OutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
- OutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.OutputNameStyle
- OutputPattern - Class in org.anchoranalysis.io.generator.sequence.pattern
-
How the output of the sequence looks on the filesystem and in the manifest.
- OutputPattern(Optional<String>, IndexableOutputNameStyle, boolean, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPattern
- OutputPatternIntegerSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern
-
A
OutputPatternthat outputs a file-name with a trailing integer index. - OutputPatternIntegerSuffix(String, boolean) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix
-
Creates in a subdirectory, using the outputName as both the subdirectory name and the prefix.
- OutputPatternIntegerSuffix(String, boolean, String, int, boolean, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix
-
Creates with a full set of flexibility about how the filename appears and whether a subdirectory is used.
- OutputPatternIntegerSuffix(String, int, boolean, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix
-
Like
OutputPatternIntegerSuffix(String, boolean)but with additional options on the manifest-folder description and whether to check outputs against rules. - OutputPatternIntegerSuffix(String, String) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix
-
Creates in a subdirectory, using the output-name as the subdirectory name, and a specific prefix.
- OutputPatternIntegerSuffix(String, String, int, boolean, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternIntegerSuffix
-
Like
OutputPatternIntegerSuffix(String, String)but with additional options about the number of digits, the manifest-folder description and whether to check outputs against rules. - OutputPatternStringSuffix - Class in org.anchoranalysis.io.generator.sequence.pattern
-
A
OutputPatternthat outputs a file-name with a trailing string index. - OutputPatternStringSuffix(String, boolean) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternStringSuffix
-
Creates without a prefix.
- OutputPatternStringSuffix(String, boolean, String) - Constructor for class org.anchoranalysis.io.generator.sequence.pattern.OutputPatternStringSuffix
-
Creates with a prefix.
- outputSelectParam(CommandLine, String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory
-
Can point to either: a path ending in .xml, assumed to BeanXML for an output manager a directory, set as the outputDirectory in the input-context
- outputsEnabled() - Method in class org.anchoranalysis.io.output.outputter.Outputter
- OutputSequence - Interface in org.anchoranalysis.io.generator.sequence
-
A sequence of elements that are written to the same directory.
- OutputSequenceFactory<T> - Class in org.anchoranalysis.io.generator.sequence
-
Creates and starts a
OutputSequencewith a particular generator and context. - OutputSequenceFactory(Generator<T>, OutputterChecked) - Constructor for class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
- OutputSequenceIncrementing<T> - Class in org.anchoranalysis.io.generator.sequence
-
A sequence of outputs that use the same generator, where each output increments an index by one in the filename.
- OutputSequenceIncrementing(BoundOutputter<T>, int) - Constructor for class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing
- OutputSequenceIndexed<T,S> - Class in org.anchoranalysis.io.generator.sequence
-
A sequence of outputs that use the same generator with non-incrementing indexes for each output.
- outputSharedObjects(MPPInitParams, OutputterChecked) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
- OutputtedFile - Class in org.anchoranalysis.io.manifest.file
-
An entry in a
Manifestfor an outputted file from an experiment. - OutputtedFile(MutableDirectory, String, String, String, Optional<ManifestDescription>) - Constructor for class org.anchoranalysis.io.manifest.file.OutputtedFile
- OutputtedFile(MutableDirectory, String, String, String, ManifestDescription) - Constructor for class org.anchoranalysis.io.manifest.file.OutputtedFile
- Outputter - Class in org.anchoranalysis.io.output.outputter
-
Like
OutputterCheckedbut exceptions are reported in aErrorReporter. - Outputter(OutputterChecked, ErrorReporter) - Constructor for class org.anchoranalysis.io.output.outputter.Outputter
- OutputterChecked - Class in org.anchoranalysis.io.output.outputter
-
A particular directory on the filesystem in which outputting can occur.
- OutputterDirectories - Class in org.anchoranalysis.mpp.segment.define
-
Directories into which collections of different types of objects are written to in a define experiment
- OutputterTarget - Class in org.anchoranalysis.io.output.outputter.directory
-
The directory and prefix an outputter writes to.
- OutputterTarget(DirectoryWithPrefix, boolean) - Constructor for class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
- outputToWriter(PrintWriter) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
- outputToWriter(PrintWriter) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- OutputWriteFailedException - Exception in org.anchoranalysis.io.output.error
- OutputWriteFailedException(String) - Constructor for exception org.anchoranalysis.io.output.error.OutputWriteFailedException
- OutputWriteFailedException(String, AnchorCombinableException) - Constructor for exception org.anchoranalysis.io.output.error.OutputWriteFailedException
- OutputWriteFailedException(String, HasFriendlyErrorMessage) - Constructor for exception org.anchoranalysis.io.output.error.OutputWriteFailedException
- OutputWriteFailedException(Throwable) - Constructor for exception org.anchoranalysis.io.output.error.OutputWriteFailedException
- OutputWriteSettings - Class in org.anchoranalysis.io.output.bean
-
Settings for how to write output, including default writers.
- OutputWriteSettings() - Constructor for class org.anchoranalysis.io.output.bean.OutputWriteSettings
- outsideAtThreshold - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3
- OutsideRange - Class in org.anchoranalysis.plugin.image.feature.bean.score
- OutsideRange() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
- OverlapCalculator - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
Calculates overlap between object-masks
- OverlapMaskBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
- OverlapMaskBase() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
- OverlapMIPBase - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
- OverlapMIPBase() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMIPBase
- OverlapNumVoxels - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
- OverlapNumVoxels() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapNumVoxels
- OverlapNumVoxelsMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
- OverlapNumVoxelsMask() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapNumVoxelsMask
- overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
- overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
- overlappingNumVoxels(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMIPBase
- OverlappingObject<T> - Class in org.anchoranalysis.image.core.object.label
-
An object-mask that is founded to overlap with another during labelling.
- OverlappingObject(T, ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.label.OverlappingObject
- OverlapRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
- OverlapRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatio
- OverlapRatioMask - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap
- OverlapRatioMask() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatioMask
- OverlapRelative - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
Expresses the number of intersecting pixels between two objects as a ratio to something else (denominator)
- OverlapRelative() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelative
- OverlapRelativeToFirst - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
- OverlapRelativeToFirst() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToFirst
- OverlapRelativeToMaxVolume - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
-
Overlap ratio to the maximum number of pixels
- OverlapRelativeToMaxVolume() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMaxVolume
- OverlapRelativeToMerged - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
- OverlapRelativeToMerged() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToMerged
- OverlapRelativeToSecond - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap
- OverlapRelativeToSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.OverlapRelativeToSecond
- overlapScoreFor(ObjectMask, ObjectMask) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.RemoveOverlappingObjects
- overlapScoreFor(BoundingBox, BoundingBox) - Method in class org.anchoranalysis.plugin.image.bean.box.RemoveOverlappingBoundingBoxes
-
The Intersection over Union (IoU) score for two bounding-boxes
- overlapScoreFor(T, T) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
-
A score calculating the overlap between two elements.
- OverlapUtilities - Class in org.anchoranalysis.mpp.overlap
- overlapWith(VoxelizedMarkMemo, VoxelizedMarkMemo, int) - Static method in class org.anchoranalysis.mpp.overlap.OverlapUtilities
- overlapWithGlobalMask(SessionInput<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
- overlapWithMaskGlobal(VoxelizedMarkMemo, VoxelizedMarkMemo, int, Voxels<UnsignedByteBuffer>, byte) - Static method in class org.anchoranalysis.mpp.overlap.OverlapUtilities
-
Counts the number of overlapping voxels between two
VoxelizedMarkMemo - Overlay - Class in org.anchoranalysis.image.bean.spatial.arrange
- Overlay - Class in org.anchoranalysis.overlay
- Overlay() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Overlay
- Overlay() - Constructor for class org.anchoranalysis.overlay.Overlay
- overlayBufferedImage(BufferedImage, BufferedImage, int, int) - Static method in class org.anchoranalysis.image.core.stack.bufferedimage.BufferedImageOverlay
- OverlayCollection - Class in org.anchoranalysis.overlay.collection
- OverlayCollection() - Constructor for class org.anchoranalysis.overlay.collection.OverlayCollection
- OverlayCollection(Stream<Overlay>) - Constructor for class org.anchoranalysis.overlay.collection.OverlayCollection
- OverlayCollectionMarkFactory - Class in org.anchoranalysis.mpp.overlay
-
Two-way factory.
- OverlayCollectionObjectFactory - Class in org.anchoranalysis.overlay.collection
-
Two-way factory.
- OverlayMark - Class in org.anchoranalysis.mpp.overlay
- OverlayMark(Mark, RegionMembershipWithFlags) - Constructor for class org.anchoranalysis.mpp.overlay.OverlayMark
- OverlayObjectMask - Class in org.anchoranalysis.overlay.object
- OverlayObjectMask(ObjectMask, int) - Constructor for class org.anchoranalysis.overlay.object.OverlayObjectMask
- OverlayProperties - Class in org.anchoranalysis.overlay
- OverlayProperties() - Constructor for class org.anchoranalysis.overlay.OverlayProperties
P
- Padding - Class in org.anchoranalysis.image.bean.spatial
-
Padding (whitespace of certain extent) placed around an object in XY direction and in Z direction.
- Padding() - Constructor for class org.anchoranalysis.image.bean.spatial.Padding
- PairedWithMask - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shared
-
Evaluates the object as a pair-feature together with the binary-mask from the shard objects.
- PairedWithMask() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
- PairNeighbors - Class in org.anchoranalysis.plugin.image.feature.bean.object.combine
-
Creates a set of features, that creates pairs of neighboring-objects and applies a mixture of single-object features and pair features.
- PairNeighbors() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
- PairPxlMarkMemo - Class in org.anchoranalysis.mpp.pair
- PairPxlMarkMemo(VoxelizedMarkMemo, VoxelizedMarkMemo) - Constructor for class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
- PairsTableCalculator - Class in org.anchoranalysis.image.feature.session.merged
-
A feature-session to evaluate pairs of objects.
- PairsTableCalculator(MergedPairsFeatures) - Constructor for class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
- PairsTableCalculator(MergedPairsFeatures, MergedPairsInclude, boolean) - Constructor for class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
- Pairwise - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
- Pairwise() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
- ParallelProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor
-
Executes jobs in parallel
- ParallelProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
- Param<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.operator.feature.bean
-
Extracts a key-value-param as a double
- Param() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.Param
- ParametersAsFeatures<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
-
Loads a
KeyValueParamsas features. - ParametersAsFeatures() - Constructor for class org.anchoranalysis.feature.bean.list.ParametersAsFeatures
- ParametersExperiment - Class in org.anchoranalysis.experiment.task
-
Parameters for executing a task, when the manifest, log etc.
- ParametersExperiment(ExperimentExecutionArguments, String, Optional<Manifest>, OutputterChecked, PathPrefixer, StatefulMessageLogger, boolean) - Constructor for class org.anchoranalysis.experiment.task.ParametersExperiment
- ParametersUnbound<T,S> - Class in org.anchoranalysis.experiment.task
- ParametersUnbound(ParametersExperiment, T, S, boolean) - Constructor for class org.anchoranalysis.experiment.task.ParametersUnbound
- ParamFromCollection<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.shared
-
Retrieves a parameter from a collection in shared-objects.
- ParamFromCollection() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
- params() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- ParamsBean<T> - Class in org.anchoranalysis.bean.shared.params
- ParamsBean() - Constructor for class org.anchoranalysis.bean.shared.params.ParamsBean
- paramsDeriver() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
- ParamsInitializer<T> - Interface in org.anchoranalysis.bean.initializable.params
- parseAndRun(String[], LauncherConfig) - Method in class org.anchoranalysis.launcher.parser.ParseArgumentsAndRunExperiment
-
Parses the arguments to a command-line experiment and runs an experiment
- ParseArgumentsAndRunExperiment - Class in org.anchoranalysis.launcher.parser
-
A general parser for command-line applications with certain attributes.
- ParseArgumentsAndRunExperiment(Logger) - Constructor for class org.anchoranalysis.launcher.parser.ParseArgumentsAndRunExperiment
- ParsedFilePathBag - Class in org.anchoranalysis.plugin.io.multifile
- ParsedFilePathBag() - Constructor for class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
- PartitionedMarks - Class in org.anchoranalysis.plugin.mpp.segment.optimization
-
Binary partition of marks into "available" and "accepted"
- PartitionedMarks(MarkCollection, ToDoubleFunction<Mark>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
-
Constructor
- path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.FilePath
- path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
- path(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.StaticFilePath
- path(String) - Static method in class org.anchoranalysis.io.manifest.finder.match.DirectoryMatch
- pathCreator() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
- PathCreator - Interface in org.anchoranalysis.io.output.path.prefixer
-
Converts file-paths between relative and absolute.
- pathCurrentJAR(Class<?>) - Static method in class org.anchoranalysis.launcher.PathCurrentJarUtilities
-
Determines the path to the current jar directory (or folder with class files) so we can resolve a properties file
- PathCurrentJarUtilities - Class in org.anchoranalysis.launcher
- PathDifference - Class in org.anchoranalysis.core.system.path
-
Calculates the "difference" between a path and a base
- PathDifferenceException - Exception in org.anchoranalysis.core.system.path
- PathDifferenceException(String) - Constructor for exception org.anchoranalysis.core.system.path.PathDifferenceException
- PathDifferenceException(String, Exception) - Constructor for exception org.anchoranalysis.core.system.path.PathDifferenceException
- pathForBinding() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
- pathForBinding() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- pathForBinding() - Method in class org.anchoranalysis.mpp.io.input.StackWithMap
- pathForBinding() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
- pathForBinding() - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertChannelsInputToStack
- pathForBinding() - Method in class org.anchoranalysis.plugin.io.manifest.CoupledManifests
- pathForBinding() - Method in class org.anchoranalysis.plugin.io.manifest.ManifestCouplingDefinition
- pathForBinding() - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.FromCSVInput
- pathFromArgument(String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.ArgumentConverter
-
Converts the string passed as a command-line argument to a path.
- PathFromGenerator - Class in org.anchoranalysis.plugin.annotation.bean.strategy
- pathOrDirectory(String[], boolean) - Static method in class org.anchoranalysis.launcher.executor.selectparam.io.OutputFactory
-
If the argument is a path to a directory, then this directory is set as the default.
- pathOrDirectoryOrGlobOrExtension(String[]) - Static method in class org.anchoranalysis.launcher.executor.selectparam.io.InputFactory
- pathOrTaskName(String[], Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.task.TaskFactory
-
If the argument a name (no extension, no root, no special-chars apart from forward-slashes), then construct an automatic path to the tasks in the configuration directory.
- pathOrTaskNameOrDefault(CommandLine, String, Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory
-
Can point to either a path to beanXML
- PathPrefixer - Class in org.anchoranalysis.io.output.bean.path.prefixer
- PathPrefixer() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
- PathPrefixerAvoidResolve - Class in org.anchoranalysis.io.output.bean.path.prefixer
-
A file-path-resolver that adds additional methods that perform the same function but output a relative-path rather than an absolute path after fully resolving paths
- PathPrefixerAvoidResolve() - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
- PathPrefixerAvoidResolve(String) - Constructor for class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
- PathPrefixerException - Exception in org.anchoranalysis.io.output.path.prefixer
- PathPrefixerException(String) - Constructor for exception org.anchoranalysis.io.output.path.prefixer.PathPrefixerException
- PathPrefixerException(Throwable) - Constructor for exception org.anchoranalysis.io.output.path.prefixer.PathPrefixerException
- PathRegEx - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
-
Matches a regex against incoming file-paths to form a prefix for output
- PathRegEx() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.PathRegEx
- pathRelativeProperties() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
-
path to a property file that defines a relative-path to the default experiment in bean XML
- pathRelativeToBean(AnchorBean<?>, String) - Static method in class org.anchoranalysis.bean.xml.factory.BeanPathUtilities
- PatternSpan - Class in org.anchoranalysis.plugin.io.bean.descriptivename.patternspan
-
Finds a pattern in the descriptive name, and uses the region from the first variable to the last-variable as the descriptive-name
- PatternSpan() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.patternspan.PatternSpan
- PayloadCalculator - Interface in org.anchoranalysis.image.feature.evaluator
- percentAnnotatedImages() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- percentGreaterEqualTo(int) - Method in class org.anchoranalysis.math.histogram.Histogram
- percentLeftMatched() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- percentRightMatched() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- percentSkippedAnnotations() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationGroup
- performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.AddConstant
- performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantBase
-
The binary arithmetic operation that combines the voxel-value and the constant-value
- performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MultiplyConstant
- performBinaryOperation(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractFromConstant
- periodEnd(Reporting<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiver
- periodEnd(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverList
- PeriodicSubdirectoryReporter<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
- PeriodicSubdirectoryReporter() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
- PeriodReceiver<T> - Interface in org.anchoranalysis.mpp.segment.optimization.feedback.period
- PeriodReceiverException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback.period
- PeriodReceiverException() - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverException
- PeriodReceiverException(Exception) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverException
- PeriodReceiverException(String) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverException
- PeriodReceiverList<T> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.period
- PeriodReceiverList() - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverList
- periodStart(Reporting<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiver
- periodStart(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodReceiverList
- PeriodTriggerBank<S> - Class in org.anchoranalysis.mpp.segment.optimization.feedback.period
- PeriodTriggerBank() - Constructor for class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodTriggerBank
- permissive() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters
-
A writer that allows all output-names, and records the written output-names
- Permissive - Class in org.anchoranalysis.io.output.bean.rules
-
Allows all output-names to be outputted in both first and second level.
- Permissive() - Constructor for class org.anchoranalysis.io.output.bean.rules.Permissive
- PermissiveExcept - Class in org.anchoranalysis.io.output.bean.rules
-
All outputs are enabled except particular ones.
- PermissiveExcept() - Constructor for class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
- PermissiveExcept(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.rules.PermissiveExcept
-
Create with first-level output names
- PermutationSetter - Interface in org.anchoranalysis.bean.permute.setter
-
Imposes a permutation on some property of a bean.
- PermutationSetterException - Exception in org.anchoranalysis.bean.permute.setter
- PermutationSetterException(String) - Constructor for exception org.anchoranalysis.bean.permute.setter.PermutationSetterException
- PermutationSetterList - Class in org.anchoranalysis.bean.permute.setter
-
Applies several permutation setters to the same object
- PermutationSetterList() - Constructor for class org.anchoranalysis.bean.permute.setter.PermutationSetterList
- PermutationSetterSingle - Class in org.anchoranalysis.bean.permute.setter
-
Sets a permutation from a list of fields
- PermutationSetterSingle() - Constructor for class org.anchoranalysis.bean.permute.setter.PermutationSetterSingle
- PermutationSetterSingle(Field) - Constructor for class org.anchoranalysis.bean.permute.setter.PermutationSetterSingle
- PermutationSetterUtilities - Class in org.anchoranalysis.bean.permute.setter
- Permute - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Permutes some changes over an
ObjectCollectionProviderand collects all the results in anObjectCollection - Permute() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Permute
- PermuteDivideByParam<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
-
Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
- PermuteDivideByParam() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteDivideByParam
- PermuteFeature<S,T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
-
Permutes one or more properties of a Feature, so as to create a set of Features
- PermuteFeature() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
- PermuteFeatureBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
-
Creates permutations of a feature by modifying a particular property of it in different ways.
- PermuteFeatureBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
- PermuteFeatureSequenceInteger<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
-
Permutes a property on a feature with a sequence of integers.
- PermuteFeatureSequenceInteger() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
- PermuteFirstSecondOrder<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
- PermuteFirstSecondOrder(PermuteFirstSecondOrder.CreateFirstSecondOrder<T>, double, double) - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
- PermuteFirstSecondOrder.CreateFirstSecondOrder<T extends FeatureInput> - Interface in org.anchoranalysis.plugin.image.feature.bean.list.permute
- PermuteGaussianScore<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
-
Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
- PermuteGaussianScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteGaussianScore
- PermuteProperty<T> - Class in org.anchoranalysis.bean.permute.property
- PermuteProperty() - Constructor for class org.anchoranalysis.bean.permute.property.PermuteProperty
- PermutePropertyDescribeIndex - Class in org.anchoranalysis.bean.permute.property
-
Proxies an existing PermuteProperty but replaces the existing naming behaviour
- PermutePropertyDescribeIndex() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
- PermutePropertyDoubleSet - Class in org.anchoranalysis.bean.permute.property
- PermutePropertyDoubleSet() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
- PermutePropertySequence<T> - Class in org.anchoranalysis.bean.permute.property
-
Base class for permute-properties involving a sequence of numbers
- PermutePropertySequence() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequence
- PermutePropertySequenceDouble - Class in org.anchoranalysis.bean.permute.property
-
An arithmetic sequence of doubles, obtained by dividing an integer sequence by a divider
- PermutePropertySequenceDouble() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
- PermutePropertySequenceDouble.DoubleRange - Class in org.anchoranalysis.bean.permute.property
- PermutePropertySequenceInteger - Class in org.anchoranalysis.bean.permute.property
-
An arithmetic sequence of doubles, obtained by dividing an integer sequence by a divider
- PermutePropertySequenceInteger() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
- PermutePropertySequenceIntegerWithinString - Class in org.anchoranalysis.bean.permute.property
- PermutePropertySequenceIntegerWithinString() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
- PermutePropertyStringSet - Class in org.anchoranalysis.bean.permute.property
- PermutePropertyStringSet() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
- PermutePropertyWithPath<T> - Class in org.anchoranalysis.bean.permute.property
-
Base classes for PermuteProperty that require a path
- PermutePropertyWithPath() - Constructor for class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
- PermuteZScore<T extends FeatureInputParams> - Class in org.anchoranalysis.plugin.image.feature.bean.list.permute
-
Similar to FeatureListProviderPermute but embeds the feature in a GaussianScore
- PermuteZScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteZScore
- Plot<T> - Class in org.anchoranalysis.plot.bean
-
Defines a plot as a function of data and axis-limits.
- Plot() - Constructor for class org.anchoranalysis.plot.bean.Plot
- PlotAxisLabels - Class in org.anchoranalysis.plot.index
-
Labels for x and y axis in graph
- PlotAxisLabels() - Constructor for class org.anchoranalysis.plot.index.PlotAxisLabels
- PlotColorScheme - Class in org.anchoranalysis.plot.bean.colorscheme
- PlotColorScheme() - Constructor for class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- PlotHistogram - Class in org.anchoranalysis.plugin.image.bean.stack.provider.plot
-
Plots a histogram onto a stack.
- PlotHistogram() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
- PlotIndexBase<T,S extends org.jfree.data.general.Dataset> - Class in org.anchoranalysis.plot.index
- PlotIndexBase(String, String[]) - Constructor for class org.anchoranalysis.plot.index.PlotIndexBase
-
Constructor
- PlotIndexBaseCategorical<T,S extends org.jfree.data.category.CategoryDataset> - Class in org.anchoranalysis.plot.index
-
Base class for plots involving categorical data types.
- PlotIndexBaseCategorical(String, String[], GetForSeries<T, String>, GetForSeries<T, Paint>) - Constructor for class org.anchoranalysis.plot.index.PlotIndexBaseCategorical
- PlotInstance - Class in org.anchoranalysis.plot
-
A
Plotcombined with data and parameters, ready to be displayed. - PlotInstance(JFreeChart, Optional<AxisLimits>) - Constructor for class org.anchoranalysis.plot.PlotInstance
- pluralize(String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities
-
Given something, returns somethings
- pluralizeMaybe(long, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities
-
Returns something or somethings depending on the number
- PNG - Class in org.anchoranalysis.io.imagej.bean.stack.writer
-
Writes a PNG image using ImageJ.
- PNG() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.PNG
- point(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains
-
Is this point within the bounding-box?
- Point2d - Class in org.anchoranalysis.spatial.point
- Point2d() - Constructor for class org.anchoranalysis.spatial.point.Point2d
- Point2d(double, double) - Constructor for class org.anchoranalysis.spatial.point.Point2d
- Point2d(Point2d) - Constructor for class org.anchoranalysis.spatial.point.Point2d
- Point2f - Class in org.anchoranalysis.spatial.point
- Point2f() - Constructor for class org.anchoranalysis.spatial.point.Point2f
- Point2f(float, float) - Constructor for class org.anchoranalysis.spatial.point.Point2f
- Point2i - Class in org.anchoranalysis.spatial.point
- Point2i() - Constructor for class org.anchoranalysis.spatial.point.Point2i
- Point2i(int, int) - Constructor for class org.anchoranalysis.spatial.point.Point2i
- Point2i(Point2i) - Constructor for class org.anchoranalysis.spatial.point.Point2i
-
Copy constructor.
- Point3d - Class in org.anchoranalysis.spatial.point
- Point3d() - Constructor for class org.anchoranalysis.spatial.point.Point3d
- Point3d(double, double, double) - Constructor for class org.anchoranalysis.spatial.point.Point3d
- Point3d(Point3f) - Constructor for class org.anchoranalysis.spatial.point.Point3d
- Point3d(Tuple3d) - Constructor for class org.anchoranalysis.spatial.point.Point3d
- Point3d(Vector3d) - Constructor for class org.anchoranalysis.spatial.point.Point3d
- Point3f - Class in org.anchoranalysis.spatial.point
- Point3f() - Constructor for class org.anchoranalysis.spatial.point.Point3f
- Point3f(float, float, float) - Constructor for class org.anchoranalysis.spatial.point.Point3f
- Point3f(Point3f) - Constructor for class org.anchoranalysis.spatial.point.Point3f
- Point3i - Class in org.anchoranalysis.spatial.point
- Point3i() - Constructor for class org.anchoranalysis.spatial.point.Point3i
-
Creates the points with a 0 in each dimension
- Point3i(int, int, int) - Constructor for class org.anchoranalysis.spatial.point.Point3i
- Point3i(ReadableTuple3i) - Constructor for class org.anchoranalysis.spatial.point.Point3i
- PointClipper - Class in org.anchoranalysis.mpp.points
-
Ensures a point has values contained inside image-dimensions
- PointConverter - Class in org.anchoranalysis.spatial.point
-
Conversion utilities between different types and dimensionalities of points
- pointIgnoreZ(Point3i) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains
-
Is this point within the bounding-box, but ignoring the z-dimension?
- PointList - Class in org.anchoranalysis.mpp.mark.points
- PointList() - Constructor for class org.anchoranalysis.mpp.mark.points.PointList
- PointList(Stream<Point3d>) - Constructor for class org.anchoranalysis.mpp.mark.points.PointList
- pointListAtFirstPoint(List<Point3i>) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
-
Sets all points in a list, to point at the first point (the root point) in the list
- PointListBase - Class in org.anchoranalysis.mpp.mark.points
- PointListBase() - Constructor for class org.anchoranalysis.mpp.mark.points.PointListBase
- PointListBase(Stream<Point3d>) - Constructor for class org.anchoranalysis.mpp.mark.points.PointListBase
- PointListFactory - Class in org.anchoranalysis.mpp.mark.points
- pointOnOutline(Point3d, Orientation) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutline
- pointOnOutline(Point3d, Orientation) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
- PointRange - Class in org.anchoranalysis.spatial.box
-
Keeps track of the range experienced by points in the x, y and z dimensions
- PointRange() - Constructor for class org.anchoranalysis.spatial.box.PointRange
- points() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
-
The points associated with the path
- points() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
- PointSampler - Interface in org.anchoranalysis.mpp.probmap
- PointsBean<T> - Class in org.anchoranalysis.mpp.bean.points
- PointsBean() - Constructor for class org.anchoranalysis.mpp.bean.points.PointsBean
- pointsDiscrete() - Method in class org.anchoranalysis.spatial.Contour
- PointsFitter - Class in org.anchoranalysis.mpp.bean.points.fitter
- PointsFitter - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks
- PointsFitter() - Constructor for class org.anchoranalysis.mpp.bean.points.fitter.PointsFitter
- PointsFitter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.PointsFitter
- PointsFitterException - Exception in org.anchoranalysis.mpp.bean.points.fitter
- PointsFitterException(Exception) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.PointsFitterException
- PointsFitterException(String) - Constructor for exception org.anchoranalysis.mpp.bean.points.fitter.PointsFitterException
- PointsFitterFromObjects - Class in org.anchoranalysis.plugin.points.bean.mark.provider.collection
- PointsFitterFromObjects() - Constructor for class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
- PointsFitterToMark - Class in org.anchoranalysis.plugin.points.bean.fitter
- PointsFitterToMark() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
- pointsFromContour(ObjectMask) - Static method in class org.anchoranalysis.plugin.points.bean.contour.PointsFromContourTraverser
-
Extracts a list of points from the outline (contour) of the object-mask
- PointsFromContourTraverser - Class in org.anchoranalysis.plugin.points.bean.contour
- PointsFromMask - Class in org.anchoranalysis.image.core.points
- PointsFromObject - Class in org.anchoranalysis.image.core.points
- PointsFromObjects - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
- PointsFromObjects() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
- PointsFromOrientationProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
- PointsFromOrientationProposer() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.PointsFromOrientationProposer
- PointsInitParams - Class in org.anchoranalysis.mpp.bean.init
- PointsNeighborChecker - Class in org.anchoranalysis.image.core.points
- pointsOnAllOutlines(ObjectCollection) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities
- pointsOnOutline(ObjectMask) - Static method in class org.anchoranalysis.plugin.points.convexhull.ConvexHullUtilities
- PointsProposer - Class in org.anchoranalysis.mpp.bean.proposer
- PointsProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.PointsProposer
- PointTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
Like a
IntConsumerbut accepts two coordinates of a point as scalar arguments. - Polygon - Class in org.anchoranalysis.mpp.mark.points
- Polygon() - Constructor for class org.anchoranalysis.mpp.mark.points.Polygon
- PolygonCurve - Class in org.anchoranalysis.mpp.mark.points
- PolygonCurve() - Constructor for class org.anchoranalysis.mpp.mark.points.PolygonCurve
- populate(List<NamedBean<FeatureListProvider<FeatureInput>>>, Logger) - Method in class org.anchoranalysis.feature.shared.SharedFeaturesInitParams
- populate(PropertyInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- populate(PropertyInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.mpp.bean.init.MPPInitParams
- populate(PropertyInitializer<?>, Define, Logger) - Method in class org.anchoranalysis.mpp.bean.init.PointsInitParams
- populate(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAngle2D
- populate(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAngle3D
- populate(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.factory.RotateAxisAngle
- populate(RotationMatrix) - Method in class org.anchoranalysis.spatial.rotation.factory.RotationMatrixFactory
-
Populates a newly created matrix.
- populateFrom(Stack, Optional<Integer>, Optional<Integer>, Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.buffer.MultiBufferSized
- populateMissingFromArbitrarySlice(Stack) - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
- PopulateStoreFromDefine<V extends BeanInitParams> - Class in org.anchoranalysis.image.bean.nonbean.init
-
Helps populates a
NamedProviderStorefrom the contents of aDefine. - PopulateStoreFromDefine(Define, PropertyInitializer<?>, Logger) - Constructor for class org.anchoranalysis.image.bean.nonbean.init.PopulateStoreFromDefine
-
Constructor
- position() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
-
The position of the buffer ala
Buffer.position. - position(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
-
Assigns a new position to the buffer.
- position(int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
-
Assigns a new position to the buffer.
- Position - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
- Position() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
- PositionProposer - Class in org.anchoranalysis.mpp.bean.proposer
- PositionProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.PositionProposer
- Positive - Annotation Type in org.anchoranalysis.bean.annotation
-
The bean-field should have a value
> 0. - possibleOverlappingObjects(ObjectMask, Iterable<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
- possibleOverlappingObjects(ObjectMask, Iterable<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.RemoveOverlappingObjects
- possibleOverlappingObjects(BoundingBox, Iterable<WithConfidence<BoundingBox>>) - Method in class org.anchoranalysis.plugin.image.bean.box.RemoveOverlappingBoundingBoxes
-
As bounding box intersection test is cheap, we pass back all neighbors
- possibleOverlappingObjects(T, Iterable<WithConfidence<T>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
-
Finds a subset of
othersthat possibly overlap with thesourceelement. - precalculate(ObjectWithProperties, Dimensions) - Method in class org.anchoranalysis.overlay.bean.DrawObject
- precalculate(ColoredOverlayCollection, DrawOverlay, Dimensions, BinaryValuesByte) - Static method in class org.anchoranalysis.overlay.writer.DrawOverlay
- PrecalculationOverlay - Class in org.anchoranalysis.overlay.writer
-
Overlays with additional pre-calculations that make them quicker to draw onto a RGBStack
- PrecalculationOverlay(ObjectWithProperties) - Constructor for class org.anchoranalysis.overlay.writer.PrecalculationOverlay
- precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
- precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
- precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
- precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
- precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
-
A precondition, which if evaluates to false, cancels the filter i.e.
- precondition(ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
- predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
- predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfNotEmpty
- predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
- predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
-
If this evaluates true, the mask will be returned as-is, otherwise
maskElseis returned - predicate(Mask) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
- PredicateAtCorner - Class in org.anchoranalysis.image.voxel.extracter.predicate
-
Projects a
VoxelsPredicateto a corner in a larger global space - PredicateAtCorner(ReadableTuple3i, VoxelsPredicate) - Constructor for class org.anchoranalysis.image.voxel.extracter.predicate.PredicateAtCorner
- PredicateBufferBinary<T> - Interface in org.anchoranalysis.image.voxel.iterator.predicate.buffer
-
Like
ProcessBufferBinarybut returns a boolean. - PredicateImplementation<T> - Class in org.anchoranalysis.image.voxel.extracter.predicate
-
Implementation of
VoxelsPredicatefor a particularVoxels. - PredicateImplementation(Voxels<T>, Predicate<T>) - Constructor for class org.anchoranalysis.image.voxel.extracter.predicate.PredicateImplementation
- PredicateTwoBytes - Interface in org.anchoranalysis.image.voxel.iterator.predicate
-
Like
Predicatebut takes two bytes as argument. - prefer(Class<? extends FeatureInput>, Class<? extends FeatureInput>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType
-
Prefer to keep descriptor whose input-class is a sub-class rather than a super-class
- prefer(Feature<?>, Feature<?>) - Static method in class org.anchoranalysis.feature.input.FeatureInputType
-
Like
FeatureInputType.prefer(Class, Class)but accepts features directly as input. - prefixPluralize(long, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities
-
Returns n somethings
- prefixPluralizeMaybe(long, String) - Static method in class org.anchoranalysis.core.value.LanguageUtilities
-
Returns 1 something or n somethings as is appropriate
- Prepend - Class in org.anchoranalysis.bean.shared.color.scheme
- Prepend() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Prepend
- PrependName - Class in org.anchoranalysis.feature.bean.list
-
Prepends a string to each feature in the list
- PrependName() - Constructor for class org.anchoranalysis.feature.bean.list.PrependName
- PreserveName - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
- PreserveName() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.PreserveName
- prettyPath(String) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.PrettyPathConverter
-
Converts to either a normalized absolute-path or relative-path depending on which is prettier to the user
- prettyPath(Path) - Static method in class org.anchoranalysis.launcher.executor.selectparam.path.PrettyPathConverter
-
Converts to either a normalized absolute-path or relative-path depending on which is prettier to the user
- PrettyPathConverter - Class in org.anchoranalysis.launcher.executor.selectparam.path
- previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
- previousEqualIndex(int) - Method in interface org.anchoranalysis.core.index.bounded.BoundedRangeIncomplete
- previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
- previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
- previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
- previousEqualIndex(int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
- previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundedIndexContainerFromList
- previousIndex(int) - Method in interface org.anchoranalysis.core.index.bounded.BoundedRangeIncomplete
- previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.BoundsFromRange
- previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.bridge.BoundedIndexContainerBridge
- previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.IntegerSequenceContaner
- previousIndex(int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
- primaryReport() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.StateReporter
- primaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterIdentity
- primaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
- primaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
- PrimitiveConverter - Class in org.anchoranalysis.image.voxel.buffer.primitive
-
Type conversion between primitive data types.
- PrincipalAxisEccentricity - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
Calculates the eccentricity of the Principal Axes (as defined by Image Moments)
- PrincipalAxisEccentricity() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisEccentricity
- PrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
The length of a principal-axis (as defined by Image Moments).
- PrincipalAxisLength() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisLength
- PrincipalAxisOrientation - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
An element from orientation of a principal-axis (as defined by Image Moments).
- PrincipalAxisOrientation() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
- printAllFilesFromTestFolderPath(String) - Method in class org.anchoranalysis.test.TestLoader
-
Prints the names of all files (recursively) in a test-folder to stdout
- PrioritisedVertex - Class in org.anchoranalysis.plugin.image.object.merge.priority
-
A vertex with a priority attached, and a boolean flag as to whether it can be merged or not
- PrioritisedVertex(ObjectMask, double, double, boolean) - Constructor for class org.anchoranalysis.plugin.image.object.merge.priority.PrioritisedVertex
-
Constructor
- Prioritizer - Interface in org.anchoranalysis.plugin.image.object.merge.priority
-
Creates a priority between two vertices
- PriorityQueueIndexRangeDownhill<T> - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
-
Implements a priority queue based upon a range of values from 0 to maxValue,
- PriorityQueueIndexRangeDownhill(int) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
- ProbabilityMap - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position
-
Uses a probability field defined over the voxels to make some positions more likely than others
- ProbabilityMap() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
- probCalculator(AnnealScheme) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
- probCalculator(AnnealScheme) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
- probCalculator(AnnealScheme) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- ProbMap - Interface in org.anchoranalysis.mpp.probmap
- ProbMapObjects - Class in org.anchoranalysis.mpp.probmap
-
TODO this doesn't seem currently used.
- ProbMapObjects(ObjectCollection, Dimensions) - Constructor for class org.anchoranalysis.mpp.probmap.ProbMapObjects
- ProbWeights - Class in org.anchoranalysis.mpp.probmap
- ProbWeights() - Constructor for class org.anchoranalysis.mpp.probmap.ProbWeights
- process(byte, byte) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessTwoBytes
- process(Channel, Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
- process(Channel, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.TwoVoxelMappingBase
- process(Channel, Channel, Channel) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
- process(Channel, Channel, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MeanThreeChannels
- process(VoxelBuffer<S>, VoxelBuffer<T>) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferBinaryWithoutOffset
-
Processes a voxel location in a buffer
- process(VoxelBuffer<S>, VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferBinary
-
Processes a voxel location in a buffer
- process(VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferUnary
-
Processes a voxel location in a buffer.
- process(Point3i) - Method in interface org.anchoranalysis.image.voxel.iterator.process.ProcessPoint
- process(Point3i, VoxelBuffer<S>, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryMixed
-
Processes a voxel location in two buffers.
- process(Point3i, VoxelBuffer<T>, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.voxelbuffer.ProcessVoxelBufferUnaryWithPoint
-
Processes a voxel location in a buffer.
- process(Point3i, S, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinary
-
Processes a voxel location in two buffers.
- process(Point3i, T, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferUnary
-
Processes a voxel location in a buffer
- process(Point3i, T, T, T, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferTernary
-
Processes a voxel location in a buffer
- process(S, T) - Method in interface org.anchoranalysis.image.voxel.iterator.process.buffer.ProcessBufferBinaryWithoutOffset
-
Processes a voxel location in a buffer
- process(T) - Method in interface org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP.OperationWithInitParams
- process(T, EnergyStack) - Method in interface org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterMPPWithEnergy.OperationWithEnergyStack
- processAllPointsInNeighborhood(boolean, ProcessVoxelNeighbor<?>) - Method in interface org.anchoranalysis.image.voxel.neighborhood.Neighborhood
- ProcessBufferBinary<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer
-
Processes a 3D point like
ProcessPointbut also retrieves twoBufferfor the current z-slice. - ProcessBufferBinaryMixed<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer
-
Processes a 3D point like
ProcessPointbut also retrieves both oneVoxelBufferfor the current z-slice and oneBufferfor the current z-slice. - ProcessBufferBinaryWithoutOffset<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer
-
Processes two buffers for each z-slice jointly, without any offset or point.
- ProcessBufferTernary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer
-
Processes a 3D point like
ProcessPointbut also retrieves three buffers for the current z-slice. - ProcessBufferUnary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.buffer
-
Processes a 3D point like
ProcessPointbut also retrieves a buffer for the current z-slice. - ProcessChangedPointAbsoluteMasked<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor
-
Processes a point which has been translated (changed) relative to another point - and includes global coordinates and includes an object-mask buffer
- processEachSlice(Channel, Consumer<ImageProcessor>) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper
-
Applies a
Consumerto each slice independently of aChannel. - processEachSlice(BinaryVoxels<UnsignedByteBuffer>, Consumer<ImageProcessor>) - Static method in class org.anchoranalysis.plugin.imagej.channel.provider.FilterHelper
-
Applies a
Consumerto each slice independently of aBinaryVoxels<UnsignedByteBuffer>. - processInput(NamedChannelsForSeries, InputOutputContext) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP
- processInput(InputOutputContext, Optional<NamedProvider<Stack>>, Optional<NamedProvider<ObjectCollection>>, Optional<KeyValueParams>, DefineOutputterMPPWithEnergy.OperationWithEnergyStack<MPPInitParams, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterMPPWithEnergy
- processInput(InputForMPPBean, InputOutputContext, DefineOutputterMPPWithEnergy.OperationWithEnergyStack<ImageInitParams, S>) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterMPPWithEnergy
- processInput(MultiInput, InputProcessContext<FeatureTableCalculator<T>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- processInput(T, InputProcessContext<FeatureList<S>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
- processInput(T, InputProcessContext<S>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FeatureSource
-
Processes one input to generate features.
- processInputImage(MultiInput, InputOutputContext, DefineOutputterMPP.OperationWithInitParams<ImageInitParams>) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP
- processInputMPP(MultiInput, InputOutputContext, DefineOutputterMPP.OperationWithInitParams<MPPInitParams>) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputterMPP
- ProcessOutputOptions - Class in org.anchoranalysis.launcher.options.outputs
-
Processes command-line options relating to additional outputs.
- ProcessOutputOptions(CommandLineExtracter, ExperimentExecutionArguments) - Constructor for class org.anchoranalysis.launcher.options.outputs.ProcessOutputOptions
- processOverlapping(WithConfidence<ObjectMask>, WithConfidence<ObjectMask>, Runnable, Consumer<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
- processOverlapping(WithConfidence<T>, WithConfidence<T>, Runnable, Consumer<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
- processOverlapping(WithConfidence<T>, WithConfidence<T>, Runnable, Consumer<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
-
Processes an object that is deemed to overlap
- processPixel(UnsignedByteBuffer, int) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityByteBuffer
- processPixel(UnsignedShortBuffer, int) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityShortBuffer
- processPixel(T, int) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
- processPoint(int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighbor
-
Processes a particular point
- processPoint(int, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsolute
-
Processes a particular point
- processPoint(int, int, int, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.neighbor.ProcessChangedPointAbsoluteMasked
-
Processes a particular point
- processPoint(int, int, int, int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
- ProcessPoint - Interface in org.anchoranalysis.image.voxel.iterator.process
-
Processes a 3D point.
- processStacks(NamedStacks, Optional<String>, GroupedSharedState<Channel, RunningSumChannel>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
- processStacks(NamedStacks, Optional<String>, GroupedSharedState<Histogram, Histogram>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
- processStacks(NamedStacks, Optional<String>, GroupedSharedState<S, T>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
-
Processes one set of named-stacks.
- ProcessTwoBytes - Interface in org.anchoranalysis.image.voxel.iterator.process
-
Processes two bytes.
- ProcessVoxelBufferBinary<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
-
Processes a 3D point like
ProcessPointbut also retrieves twoVoxelBuffers for the current z-slice. - ProcessVoxelBufferBinaryWithoutOffset<S,T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
-
Processes two voxel-buffers for each z-slice jointly, without any offset or point.
- ProcessVoxelBufferUnary<T> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
-
Processes a 3D point like
ProcessPointbut also retrieves aVoxelBufferfor the current z-slice. - ProcessVoxelBufferUnaryWithPoint<T,E extends Exception> - Interface in org.anchoranalysis.image.voxel.iterator.process.voxelbuffer
-
Processes a 3D point like
ProcessVoxelBufferUnarybut also exposes aPoint3i. - ProcessVoxelNeighbor<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor
-
Processes a point that is an neighbor of another.
- ProcessVoxelNeighborAbsolute<T> - Interface in org.anchoranalysis.image.voxel.iterator.neighbor
-
Processes a point that is a neighbor of another - includes global (absolute) coordinates for this point.
- ProcessVoxelNeighborAbsoluteWithSlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.iterator.neighbor
- ProcessVoxelNeighborAbsoluteWithSlidingBuffer(SlidingBuffer<?>) - Constructor for class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
- ProcessVoxelNeighborFactory - Class in org.anchoranalysis.image.voxel.iterator.neighbor
- progressing() - Method in interface org.anchoranalysis.core.functional.checked.CheckedSupplier
-
An interface to a similar supplier that uses a progress-reporter
- ProgressReporter - Interface in org.anchoranalysis.core.progress
- ProgressReporterConsole - Class in org.anchoranalysis.core.progress
- ProgressReporterConsole(int) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterConsole
- ProgressReporterIncrement - Class in org.anchoranalysis.core.progress
- ProgressReporterIncrement(ProgressReporter) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterIncrement
- ProgressReporterMultiple - Class in org.anchoranalysis.core.progress
- ProgressReporterMultiple(ProgressReporter, int) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterMultiple
- ProgressReporterNull - Class in org.anchoranalysis.core.progress
-
Placeholder that doesn't measure any progress
- ProgressReporterOneOfMany - Class in org.anchoranalysis.core.progress
- ProgressReporterOneOfMany(ProgressReporterMultiple) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
- ProgressReporterOneOfMany(ProgressReporterMultiple, int, int) - Constructor for class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
- projectMax() - Method in class org.anchoranalysis.image.core.channel.Channel
- projectMax() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
-
Maximum-intensity projection.
- projectMax() - Method in class org.anchoranalysis.image.core.stack.Stack
-
Maximum intensity projection.
- projectMax() - Method in class org.anchoranalysis.image.core.stack.StackNotUniformSized
-
Maximum intensity projection.
- projectMax() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
A maximum-intensity projection (flattens in z dimension)
- projectMax() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
-
A maximum intensity projection of all slices
- projectMean() - Method in class org.anchoranalysis.image.core.channel.Channel
- projectMean() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
-
A mean intensity projection of all slices
- projectSlice(T) - Method in class org.anchoranalysis.image.voxel.buffer.max.MaxIntensityBuffer
- projectSlice(T) - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
- PropertyDefiner - Interface in org.anchoranalysis.bean.initializable.property
- PropertyInitializer<P> - Class in org.anchoranalysis.bean.initializable.property
-
Tries to initialize a bean's property with particular (or derived) parameters
- PropertyInitializer(Class<?>) - Constructor for class org.anchoranalysis.bean.initializable.property.PropertyInitializer
-
Simpler case where only the current-parameters can be initialized, but for no further property-types.
- PropertyInitializer(Class<?>, List<ExtractFromParam<P, ?>>) - Constructor for class org.anchoranalysis.bean.initializable.property.PropertyInitializer
-
More complex-case where both current-parameters and other extracted property-types can be initialized.
- propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermuteProperty
-
An iterator (of size numPermutations()) with the values for the property
- propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
- propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
- propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
- propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
- propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
- propertyValues() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
- propertyValuesDefinitelyInteger() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceInteger
- ProposalAbnormalFailureException - Exception in org.anchoranalysis.mpp.proposer
-
An exception when a proposal could not be made for an abnormal reason
- ProposalAbnormalFailureException(String) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException
- ProposalAbnormalFailureException(String, Throwable) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException
- ProposalAbnormalFailureException(Throwable) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposalAbnormalFailureException
- proposalVisualization(boolean) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkProposer
- proposalVisualization(boolean) - Method in class org.anchoranalysis.mpp.bean.proposer.PointsProposer
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.PointsFromOrientationProposer
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- proposalVisualization(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
- proposalVisualization(boolean, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ChooseOneList
- proposalVisualization(boolean, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
- proposalVisualization(boolean, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrderedList
- propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.proposer.ScalarProposer
- propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Constant
- propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
- propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
- propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
- propose(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
- propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkCollectionProposer
- propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.CreateNew
- propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
- propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
- propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
- propose(MarkWithIdentifierFactory, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
- propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.proposer.OrientationProposer
- propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
- propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
- propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
- propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
- propose(Mark, Dimensions, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomXY
- propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkMergeProposer
- propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
- propose(VoxelizedMarkMemo, VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
- propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkProposer
- propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
- propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
- propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
- propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
- propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
- propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
- propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
- propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
- propose(VoxelizedMarkMemo, ProposerContext) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
- propose(VoxelizedMarkMemo, ProposerContext, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ChooseOneList
- propose(VoxelizedMarkMemo, ProposerContext, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
- propose(VoxelizedMarkMemo, ProposerContext, List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrderedList
- propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkSplitProposer
- propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
- propose(VoxelizedMarkMemo, ProposerContext, MarkWithIdentifierFactory) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
- propose(VoxelizedMarkMemo, ProposerContext, MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
- propose(VoxelizedMarkMemo, ProposerContext, MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
- propose(VoxelizedMarkMemo, ProposerContext, MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Repeat
- propose(ProposerContext) - Method in interface org.anchoranalysis.mpp.proposer.OptionalPointProposer
- propose(ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
- propose(ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
- propose(ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.UniformRandom
- propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class org.anchoranalysis.mpp.bean.proposer.radii.RadiiProposer
- propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
- propose(Point3d, RandomNumberGenerator, Dimensions, Orientation) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
- propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class org.anchoranalysis.mpp.bean.proposer.PointsProposer
- propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
- propose(Point3d, Mark, Dimensions, RandomNumberGenerator, ErrorNode) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- proposeKernel(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- proposeNewMarks(VoxelizedMarksWithEnergy, int, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
- proposeNewMarks(MarksFromPartition, int, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
- proposeNewMarks(T, int, KernelCalculationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
- proposer() - Method in class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
- ProposerBean<T> - Class in org.anchoranalysis.mpp.bean.proposer
- ProposerBean() - Constructor for class org.anchoranalysis.mpp.bean.proposer.ProposerBean
- ProposerContext - Class in org.anchoranalysis.mpp.proposer
- ProposerContext(RandomNumberGenerator, EnergyStack, RegionMap, ErrorNode) - Constructor for class org.anchoranalysis.mpp.proposer.ProposerContext
- ProposerException - Exception in org.anchoranalysis.mpp.proposer
-
An exception thrown when something goes wrong in a Proposer
- ProposerException(String) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposerException
- ProposerException(Throwable) - Constructor for exception org.anchoranalysis.mpp.proposer.ProposerException
- ProposerFailureDescription - Class in org.anchoranalysis.mpp.proposer.error
- ProposerFailureDescription() - Constructor for class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
- Provider<T> - Interface in org.anchoranalysis.bean.provider
-
A class (usually an
AnchorBean} that creates or provides another obhect - ProviderAsStack - Interface in org.anchoranalysis.image.core.stack
-
Provides a stack
- ProviderHolder<T> - Class in org.anchoranalysis.bean.provider
-
A convenient way of providing an object without using a
AnchorBean. - ProviderHolder(T) - Constructor for class org.anchoranalysis.bean.provider.ProviderHolder
- put(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
- put(Class<? extends T>, T) - Method in class org.anchoranalysis.bean.BeanInstanceMap
- put(String, double) - Method in class org.anchoranalysis.core.value.KeyValueParams
- put(String, String) - Method in class org.anchoranalysis.core.value.KeyValueParams
- put(String, CSVRow) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.MapGroupToRow
- put(ByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Relative put-method from an unsigned byte buffer, represented by a
ByteBuffer. - put(ShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
Relative put-method from an unsigned short buffer, represented by a
ShortBuffer. - put(K, V) - Method in class org.anchoranalysis.core.cache.LRUCache
-
Puts a key-value pair irrespective of whether its already present or not
- put(UnsignedByteBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Relative put-method from an unsigned byte buffer, represented by a
UnsignedByteBuffer. - put(UnsignedShortBuffer) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
Relative put-method from an unsigned short buffer, represented by a
UnsignedShortBuffer. - put(T, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.PriorityQueueIndexRangeDownhill
- put(U, S) - Method in class org.anchoranalysis.feature.calculate.FeatureCalculationMap
- putAll(KeyValueParams) - Method in class org.anchoranalysis.core.value.KeyValueParams
- putByte(int, byte) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
-
Puts a byte in the buffer at a particular position, converting, if necessary, to the buffer type.
- putCode(int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedIntBuffer
- putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
-
Puts a double at the current buffer position.
- putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
- putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
- putDouble(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
- putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
-
Puts a double at a particular buffer position.
- putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
- putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
- putDouble(int, double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
- putDoubleClipped(double) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Puts a double at the current buffer position, clipping to ensure the value is within the range
(0,255). - putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
-
Puts a float at the current buffer position.
- putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
- putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
- putFloat(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
- putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
-
Puts a float at a particular buffer position.
- putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
- putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
- putFloat(int, float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
- putFloatClipped(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Puts a float at the current buffer position, clipping to ensure the value is within the range
(0,255). - putFloatClipped(float) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
Puts a float at the current buffer position, clipping to ensure the value is within the range
(0,255). - putIfEmpty(String, double) - Method in class org.anchoranalysis.core.value.KeyValueParams
- putInt(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
-
Puts an int in the buffer at a particular position, converting, if necessary, to the buffer type.
- putInt(int, int) - Method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
- putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
-
Puts a long at the current buffer position.
- putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
- putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
- putLong(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
- putLongClipped(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
Puts a long at the current buffer position, clipping to ensure the value is within the range
(0,255). - putRaw(byte) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Puts an unsigned-byte (represented as a byte) at the current buffer position.
- putRaw(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
-
Puts an unsigned-int (represented as a int) at the current buffer position.
- putRaw(int, byte) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Puts an unsigned-byte (represented as a byte) a particular buffer position.
- putRaw(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
-
Puts an unsigned-int (represented as a int) a particular buffer position.
- putRaw(int, short) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
Puts an unsigned-short (represented as a short) a particular buffer position.
- putRaw(short) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
Puts an unsigned-short (represented as a short) at the current buffer position.
- putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
-
Puts an unsigned-byte (represented by an int) at current buffer position.
- putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
- putUnsigned(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
- putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
-
Puts an unsigned-byte (represented as a int) a particular buffer position.
- putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
- putUnsigned(int, int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
- putUnsigned(int, long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
-
Puts an unsigned-int (represented as a long) a particular buffer position.
- putUnsigned(long) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
-
Puts an unsigned-int (represented by a long) at current buffer position.
- putUnsignedClipped(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
Puts a long at the current buffer position, clipping to ensure the value is within the range
(0,255). - putUnsignedInt(int) - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Puts an unsigned-int (represented by a int) at current buffer position.
- PxlListOperationFromMark - Class in org.anchoranalysis.mpp.feature.bean.mark
- PxlListOperationFromMark() - Constructor for class org.anchoranalysis.mpp.feature.bean.mark.PxlListOperationFromMark
- PxlMarkMemoFactory - Class in org.anchoranalysis.mpp.mark.voxelized.memo
Q
- QuadraticEquationSolver - Class in org.anchoranalysis.math.equation
-
Solves a Quadratic Equation by finding non-complex roots
- QuadraticEquationSolver.QuadraticRoots - Class in org.anchoranalysis.math.equation
-
Roots (solution) of a quadratic equation
- QuadraticRoots(double, double) - Constructor for class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
- quantile(double) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
- quantile(double) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
- quantile(double) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
- quantile(double) - Method in class org.anchoranalysis.math.histogram.Histogram
- Quantile - Class in org.anchoranalysis.feature.bean.results
-
The quantile of the results from a particular feature.
- Quantile - Class in org.anchoranalysis.plugin.image.bean.histogram.threshold
-
Calculates the threshold value from a quantile of a histogram.
- Quantile - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- Quantile() - Constructor for class org.anchoranalysis.feature.bean.results.Quantile
- Quantile() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
- Quantile() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
- quantileAboveZero(double) - Method in class org.anchoranalysis.math.histogram.Histogram
- QuantileAcrossConnectedComponents - Class in org.anchoranalysis.plugin.image.feature.bean.stack.object
-
Calculates the median of a feature applied to each connected component
- QuantileAcrossConnectedComponents() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
- QuantileAcrossObjects<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.shared.object
-
Calculates the quantile of a feature applied to each connected component
- QuantileAcrossObjects() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
- QuantileIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel
- QuantileIntensity(double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.QuantileIntensity
- QuantileIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram
-
Scales by a quantile of the intensity values of an image.
- QuantileIntensityFromHistogram(double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.QuantileIntensityFromHistogram
- QuantileStretch - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Changes the voxel values to map the range of 0th quantile to xth quantile across the entire voxel data range
- QuantileStretch() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
- QuickBase<T extends InputFromManager> - Class in org.anchoranalysis.plugin.quick.bean.input
-
A base for quick managers that make various assumptions about file-structure.
- QuickBase() - Constructor for class org.anchoranalysis.plugin.quick.bean.input.QuickBase
- QuickExperiment<S> - Class in org.anchoranalysis.plugin.quick.bean.experiment
-
A quick way of defining an InputOutputExperiment where several assumptions are made.
- QuickExperiment() - Constructor for class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- QuickMultiDatasetExperiment<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.quick.bean.experiment
-
Makes a lot of assumptions, that allows us to reduce the number of inputs to an
InputOutputExperiment. - QuickMultiDatasetExperiment() - Constructor for class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- QuickMultiDatasetStructuredExperiment<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.quick.bean.structure
-
Similar to
QuickMultiDatasetStructuredExperimentput sets properties according to an expected directory structure. - QuickMultiDatasetStructuredExperiment() - Constructor for class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- quickOverlap() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- quickOverlap() - Method in class org.anchoranalysis.mpp.mark.Mark
-
An alternative "quick" metric for overlap for a mark
- QuickOverlapCalculation - Interface in org.anchoranalysis.mpp.mark
-
A method to quickly calculate overlap approximately
R
- RadiiMinRatio - Class in org.anchoranalysis.plugin.mpp.bean.check
- RadiiMinRatio() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
- radiiOrdered() - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
- radiiOrderedResolved(Optional<Resolution>) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
- RadiiProposer - Class in org.anchoranalysis.mpp.bean.proposer.radii
- RadiiProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.radii.RadiiProposer
- RadiiProposerRepeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.radii
- RadiiProposerRepeat() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
- RadiiRandomizer - Class in org.anchoranalysis.mpp.mark.conic
-
Utility functions for generating random radii for
ConicBase - RadiiRatio - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.radii
- RadiiRatio() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
- radiusForRegion(int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- radiusForRegionSquared(int) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- RandomCollection<T> - Class in org.anchoranalysis.mpp.pair
-
A collection of items from which one can randomly sample
- RandomCollection() - Constructor for class org.anchoranalysis.mpp.pair.RandomCollection
- RandomCollectionWithAddCriteria<T> - Class in org.anchoranalysis.mpp.feature.addcriteria
-
An implementation of a
RandomCollectionthat usesAddCriteria - RandomCollectionWithAddCriteria(Class<?>) - Constructor for class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- randomIndex(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- randomizeRadii(Bound, RandomNumberGenerator, Optional<Resolution>, boolean) - Static method in class org.anchoranalysis.mpp.mark.conic.RadiiRandomizer
- randomMark(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- RandomNumberGenerator - Interface in org.anchoranalysis.core.random
-
Generates random numbers from various distributions.
- RandomNumberGeneratorBean - Class in org.anchoranalysis.bean.shared.random
- RandomNumberGeneratorBean() - Constructor for class org.anchoranalysis.bean.shared.random.RandomNumberGeneratorBean
- RandomNumberGeneratorMersenne - Class in org.anchoranalysis.core.random
-
Implements a random-number generator using the
MersenneTwisteralgorithm. - RandomNumberGeneratorMersenne(boolean) - Constructor for class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
- RandomOrder - Class in org.anchoranalysis.plugin.io.bean.provider.file
- RandomOrder() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.RandomOrder
- randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.bound.OrientableBounds
- randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
- randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds
- randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
- randomOrientation(RandomNumberGenerator, Optional<Resolution>) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
- RandomOrientation - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
- RandomOrientation() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
- RandomOrientation(RotationBounds) - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
- RandomXY - Class in org.anchoranalysis.plugin.mpp.bean.proposer.orientation
- RandomXY() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomXY
- randOpen(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
-
A random value between the bounds (open interval)
- range() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequence
- Range - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
-
The range (difference in values) between two quantiles
- Range<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range.feature
-
The statistical range between two values i.e.
- Range() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
- Range() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
- rangeChannelNum() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
- RangeCompareBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
- RangeCompareBase() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
- RangeCompareFromScalars<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.range
-
A base-class for setting the boundaries of the range using constant scalars
- RangeCompareFromScalars() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
- rangeCPresent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
- rangeLimitsIfEmpty(DefaultCategoryDataset) - Method in class org.anchoranalysis.plot.index.BarPlot
- rangeLimitsIfEmpty(DefaultBoxAndWhiskerCategoryDataset) - Method in class org.anchoranalysis.plot.index.BoxPlot
- rangeLimitsIfEmpty(XYDataset) - Method in class org.anchoranalysis.plot.index.LinePlot
- rangeLimitsIfEmpty(S) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
- rangeSliceNum() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
- RangeSum - Class in org.anchoranalysis.plugin.annotation.comparison
- RangeSum() - Constructor for class org.anchoranalysis.plugin.annotation.comparison.RangeSum
- rangeTimeIndex() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
- rangeTPresent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
- RasterArranger - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange
- RasterArranger() - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.RasterArranger
- rasterResizing() - Method in class org.anchoranalysis.image.voxel.interpolator.InterpolatorFactory
- RasterTask<S,U> - Class in org.anchoranalysis.image.experiment.bean.task
-
An experiment that takes (primarily) a series of raster images as an input.
- RasterTask() - Constructor for class org.anchoranalysis.image.experiment.bean.task.RasterTask
- RasterWriterDelegateBase - Class in org.anchoranalysis.plugin.io.bean.stack.writer
-
A base class for a
StackWriterdelegates to anotherStackWriterbased on values of aStackWriteOptions. - RasterWriterDelegateBase() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
- ratioBounds() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
- RatioFirstToSecond - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Ratio of first-object to second-object in a pair
- RatioFirstToSecond() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.RatioFirstToSecond
- RatioNonMode - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- RatioNonMode() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
- ratioPointsInsideRegion(Mark, List<Point3f>, RegionMap, int) - Static method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- RatioPrincipalAxisLength - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
Calculates the ratio of prinicpal-axis length using Image Moments
- RatioPrincipalAxisLength() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.RatioPrincipalAxisLength
- RatioThreshold - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
- RatioThreshold() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
- read(Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationReader
-
Reads an annotation if it can, returns null otherwise
- read(Path) - Method in class org.anchoranalysis.annotation.io.image.WholeImageLabelAnnotationReader
- read(Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationReader
- ReadableTuple3i - Interface in org.anchoranalysis.spatial.point
-
Read-only access to a tuple
- ReadAnnotationFromFile - Class in org.anchoranalysis.plugin.annotation.bean.strategy
- readAssumeExists(Path) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.ReadAnnotationFromFile
- readCheckExists(Path) - Static method in class org.anchoranalysis.plugin.annotation.bean.strategy.ReadAnnotationFromFile
- readDefaultMarks(Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationReader
- readFile(Path) - Static method in class org.anchoranalysis.io.manifest.file.TextFileReader
- readFromCSV(Path, boolean) - Static method in class org.anchoranalysis.image.experiment.label.FileLabelMap
- readFromFile(Path) - Static method in class org.anchoranalysis.core.value.KeyValueParams
- readMetadata(Path, boolean) - Static method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
-
Looks for a metadata file describing the resolution
- ReadOptions - Class in org.anchoranalysis.io.bioformats.bean.options
- ReadOptions() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
- ReadOptionsDelegate - Class in org.anchoranalysis.io.bioformats.bean.options
-
Forces a particular settings, but otherwise uses settings from a delegate
- ReadOptionsDelegate() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
- readResolutionXml(File) - Static method in class org.anchoranalysis.plugin.io.xml.ResolutionAsXml
-
Retrieves resolution from a XML file previously written by
ResolutionAsXml.writeResolutionXml(Resolution, Path). - ReadVoxelExtentXml - Class in org.anchoranalysis.plugin.io.bean.stack.reader
- ReadVoxelExtentXml() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
- reconstruction(VoxelsWrapper, VoxelsWrapper, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.grayscalereconstruction.GrayscaleReconstruction2DIJ
- reconstruction(VoxelsWrapper, VoxelsWrapper, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionByErosion
- reconstruction(VoxelsWrapper, VoxelsWrapper, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.grayscalereconstruction.GrayscaleReconstructionRobinson
- record(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
- recordedOutputs() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters
-
If defined, all output-names that are passed as arguments to both writers are recorded here.
- RecordedOutputs - Class in org.anchoranalysis.io.output.recorded
-
Outputs recorded from
RecordOutputNamesForWriter. - RecordedOutputs() - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputs
- RecordedOutputsWithRules - Class in org.anchoranalysis.io.output.recorded
-
Rules to determine what outputting occurs, together with maybe an entity that records the output-names that are used when writing / querying.
- RecordedOutputsWithRules() - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules
-
Creates with no rules or outputs defined.
- RecordedOutputsWithRules(MultiLevelRecordedOutputs, MultiLevelOutputEnabled, OutputEnabledDelta) - Constructor for class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules
-
Creates with all elements defined.
- recordError(Class<?>, String) - Method in interface org.anchoranalysis.core.log.error.ErrorReporter
-
Reports an error that occurred as a string
- recordError(Class<?>, String) - Method in class org.anchoranalysis.core.log.error.ErrorReporterIntoLog
- recordError(Class<?>, String) - Method in class org.anchoranalysis.experiment.task.ErrorReporterForTask
- recordError(Class<?>, Throwable) - Method in interface org.anchoranalysis.core.log.error.ErrorReporter
-
Reports an error that occurred as an exception
- recordError(Class<?>, Throwable) - Method in class org.anchoranalysis.core.log.error.ErrorReporterIntoLog
- recordError(Class<?>, Throwable) - Method in class org.anchoranalysis.experiment.task.ErrorReporterForTask
- RecordingWriters - Class in org.anchoranalysis.io.output.recorded
-
Two writers that record any output-names that are passed as arguments.
- RecordingWriters(OutputterChecked, Optional<WriterExecuteBeforeEveryOperation>, Optional<MultiLevelRecordedOutputs>) - Constructor for class org.anchoranalysis.io.output.recorded.RecordingWriters
-
Creates the two writers.
- recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
- recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in class org.anchoranalysis.io.manifest.operationrecorder.DualWriterOperationRecorder
- recordSubdirectoryCreated(Path, ManifestDirectoryDescription, SubdirectoryBase) - Method in interface org.anchoranalysis.io.manifest.operationrecorder.WriteOperationRecorder
-
Records a subdirectory that has been recated.
- recordWrittenFile(String, ManifestDescription, Path, String) - Method in class org.anchoranalysis.io.manifest.directory.JobRootDirectory
- recordWrittenFile(String, ManifestDescription, Path, String) - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
- recordWrittenFile(String, ManifestDescription, Path, String) - Method in class org.anchoranalysis.io.manifest.directory.Subdirectory
- recordWrittenFile(String, ManifestDescription, Path, String) - Method in class org.anchoranalysis.io.manifest.operationrecorder.DualWriterOperationRecorder
- recordWrittenFile(String, ManifestDescription, Path, String) - Method in interface org.anchoranalysis.io.manifest.operationrecorder.WriteOperationRecorder
-
Records a file written.
- RecursivelyDescribeExceptionStack - Class in org.anchoranalysis.core.exception.friendly
-
Generates a nice string representation of an Exception and its causes according to certain rules.
- red() - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- reduce() - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
-
Reduce the cost matrix by subtracting the smallest element of each row from all elements of the row as well as the smallest element of each column from all elements of the column.
- reduce(List<WithConfidence<ObjectMask>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
- reduce(List<WithConfidence<T>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElements
-
Reduce a list of elements (each with a confidence score) to a smaller-list.
- reduce(List<WithConfidence<T>>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
- ReduceElements<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
Reduces the number or spatial-extent of elements by favouring higher-confidence elements over lower-confidence elements.
- ReduceElements() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElements
- ReduceElementsGreedy<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
Reduces the number or spatial-extent of elements by favouring higher-confidence elements over lower-confidence elements.
- ReduceElementsGreedy() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ReduceElementsGreedy
- ReduceFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
Calculates the aggregate of a feature applied to both the first and second objects in a
FeatureInputPairObjects. - ReduceFirstAndSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceFirstAndSecond
- ReduceRatioFirstAndSecond - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
Calculates the aggregate of the ratio of
first:secondandsecond:firstfor aFeatureInputPairObjects - ReduceRatioFirstAndSecond() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.ReduceRatioFirstAndSecond
- Reference<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
- Reference - Class in org.anchoranalysis.plugin.image.bean.channel.provider
- Reference - Class in org.anchoranalysis.plugin.image.bean.histogram.provider
- Reference - Class in org.anchoranalysis.plugin.image.bean.mask.provider
- Reference - Class in org.anchoranalysis.plugin.image.bean.object.provider
- Reference - Class in org.anchoranalysis.plugin.image.bean.stack.provider
- Reference - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
- Reference - Class in org.anchoranalysis.plugin.points.bean.fitter
- Reference() - Constructor for class org.anchoranalysis.feature.bean.operator.Reference
- Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
- Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
- Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
- Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Reference
- Reference() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
- Reference() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
- Reference() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.Reference
- Reference(String) - Constructor for class org.anchoranalysis.feature.bean.operator.Reference
- Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
- Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
- Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
- Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Reference
- Reference(String) - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
- Reference(String) - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
- ReferencedFeatures<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
- ReferencedFeatures() - Constructor for class org.anchoranalysis.feature.bean.list.ReferencedFeatures
- ReferenceFactory - Class in org.anchoranalysis.plugin.image.provider
-
Creates reference (i.e.
- ReferenceOrElse - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Returns a object-collection by name if it exists, or else calls
objectsElseif it doesn't exist. - ReferenceOrElse() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
- ReferenceOrEmpty - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
-
Returns an existing marks-collection or an empty set if it doesn't exist
- ReferenceOrEmpty() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
- referenceString(Object) - Static method in class org.anchoranalysis.core.system.MemoryUtilities
- ReflectInAxesWithinDistance - Class in org.anchoranalysis.plugin.points.bean.fitter
-
Reflects points in each axes if all points are within a certain distance from it
- ReflectInAxesWithinDistance() - Constructor for class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
- reflectThroughOrigin() - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
Reflects the bounding box through the origin (i.e.
- RegEx - Class in org.anchoranalysis.bean.shared.regex
-
The regular-expression to use for matching groups.
- RegEx() - Constructor for class org.anchoranalysis.bean.shared.regex.RegEx
- RegExList - Class in org.anchoranalysis.bean.shared.regex
- RegExList() - Constructor for class org.anchoranalysis.bean.shared.regex.RegExList
- RegExMatcher - Class in org.anchoranalysis.plugin.io.bean.descriptivename
- RegExMatcher() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.RegExMatcher
- RegExpFilePathParser - Class in org.anchoranalysis.plugin.io.bean.groupfiles.parser
- RegExpFilePathParser() - Constructor for class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- RegExSimple - Class in org.anchoranalysis.bean.shared.regex
- RegExSimple() - Constructor for class org.anchoranalysis.bean.shared.regex.RegExSimple
- RegExSimple(String) - Constructor for class org.anchoranalysis.bean.shared.regex.RegExSimple
- region() - Method in interface org.anchoranalysis.annotation.mark.AnnotationWithMarks
-
The region(s) of the marks that specifies the annotation.
- region() - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
- region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.core.mask.Mask
- region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
A (sub-)region of the voxels.
- region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.extracter.Base
- region(BoundingBox, boolean) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
-
A (sub-)region of the voxels.
- region(BoundingBox, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
A (sub-)region of the object-mask.
- regionIntersecting(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Creates an object-mask covering the a bounding-box (that is required to intersect at least partially)
- regionIntersecting(BoundingBox, int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
Like
BoundedVoxels.region(org.anchoranalysis.spatial.box.BoundingBox, boolean)but only expects a bounding-box that intersects at least partially. - RegionMap - Class in org.anchoranalysis.mpp.bean.regionmap
-
Maps integer IDs to sub-regions in the map
- RegionMap() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMap
- RegionMap(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMap
- RegionMapSingleton - Class in org.anchoranalysis.mpp.bean.regionmap
- RegionMembership - Class in org.anchoranalysis.mpp.bean.regionmap
- RegionMembership() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- RegionMembership(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- RegionMembershipAnd - Class in org.anchoranalysis.mpp.bean.regionmap
- RegionMembershipAnd() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd
- RegionMembershipAnd(int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipAnd
- RegionMembershipOr - Class in org.anchoranalysis.mpp.bean.regionmap
- RegionMembershipOr() - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipOr
- RegionMembershipUtilities - Class in org.anchoranalysis.mpp.bean.regionmap
- RegionMembershipWithFlags - Class in org.anchoranalysis.mpp.bean.regionmap
- RegionMembershipWithFlags(RegionMembership, int) - Constructor for class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
- regionZ(int, int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Creates an object-mask with a subrange of the slices.
- regionZ(int, int, VoxelsFactoryTypeBound<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
Creates an box with a subrange of the slices.
- register(String, AnchorBeanFactory) - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories
-
Registers a specific factory
- register(String, CreateFromList<T>) - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories
-
Registers a bean that creates a
List<> - registerAllPackageBeanFactories() - Static method in class org.anchoranalysis.bean.xml.RegisterBeanFactories
-
Registers the factories for the beans that exist in this package
- registerBeanFactories() - Static method in class org.anchoranalysis.image.bean.RegisterBeanFactoriesImage
- RegisterBeanFactories - Class in org.anchoranalysis.bean.xml
-
Utility class for registering the Bean-factories that are found in anchor-bean (or any other)
- RegisterBeanFactoriesImage - Class in org.anchoranalysis.image.bean
-
Registers beans that needs particular factories
- rejected() - Method in interface org.anchoranalysis.annotation.mark.DualMarks
-
The rejected marks.
- RejectIfConditionXYResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader
-
If the XY resolution of an opened-image meets a certain condition then the resolution is scaled by a factor.
- RejectIfConditionXYResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
- RejectIfIntensityLessThan - Class in org.anchoranalysis.plugin.image.feature.bean.score
- RejectIfIntensityLessThan() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
- RejectIfNotConnected - Class in org.anchoranalysis.plugin.image.bean.object.provider.connected
-
Rejects a set of objects, if any object is not fully connected (pixels form two or more separate connected components)
- RejectIfNotConnected() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.connected.RejectIfNotConnected
- RejectIterationIfAllHigh - Class in org.anchoranalysis.image.voxel.object.morphological.accept
- RejectIterationIfAllHigh() - Constructor for class org.anchoranalysis.image.voxel.object.morphological.accept.RejectIterationIfAllHigh
- RejectIterationIfLowDisconnected - Class in org.anchoranalysis.image.voxel.object.morphological.accept
- RejectIterationIfLowDisconnected() - Constructor for class org.anchoranalysis.image.voxel.object.morphological.accept.RejectIterationIfLowDisconnected
- rejectProposal() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- relation() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- relation() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold
-
The relation to the threshold to consider
- relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
- relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
- relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
- relation() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
- RelationBean - Class in org.anchoranalysis.bean.shared.relation
- RelationBean() - Constructor for class org.anchoranalysis.bean.shared.relation.RelationBean
- RelationToConstant - Class in org.anchoranalysis.bean.shared.relation.threshold
- RelationToConstant() - Constructor for class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- RelationToConstant(RelationBean, double) - Constructor for class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- RelationToThreshold - Class in org.anchoranalysis.bean.shared.relation.threshold
-
A threshold and a relation to it, allowing for tests of a value in relation to a threshold.
- RelationToThreshold() - Constructor for class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold
- RelationToValue - Interface in org.anchoranalysis.math.relation
- RelationWithMatches - Class in org.anchoranalysis.plugin.image.bean.object.filter.dependent
-
Matches each object with others, and keeps only those where a relation holds true for all matches (in terms of features)
- RelationWithMatches() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
- relativeMaskTo(BoundingBox) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Creates a new object-mask with coordinates changed to be relative to another box.
- relativePath() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
- relativePath() - Method in class org.anchoranalysis.io.manifest.directory.RootDirectory
- relativePath() - Method in class org.anchoranalysis.io.manifest.directory.SubdirectoryBase
- relativePositionTo(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
The relative position of the corner to another bounding box
- relativePositionTo(Point3i, ReadableTuple3i) - Static method in class org.anchoranalysis.spatial.box.BoundingBox
- relativePositionToBox(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
A new bounding-box using relative position coordinates to another box
- relativeScale(Extent, Extent) - Static method in class org.anchoranalysis.spatial.scale.ScaleFactorUtilities
-
Calculates a scaling factor so as to scale sdSource to sdTarget
- releaseKeepBest() - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
- releaseKeepBest() - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- remove() - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble.DoubleRange
- remove(int) - Method in class org.anchoranalysis.core.color.ColorList
- remove(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- remove(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- remove(int) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
- remove(int) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- remove(int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
- remove(int) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- remove(int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- remove(int) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- remove(int) - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- remove(int, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- remove(Object) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- remove(EnergySavedInd, int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
- remove(MemoCollection, int, VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- remove(MemoCollection, VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- remove(MemoForIndex, VoxelizedMarkMemo) - Method in interface org.anchoranalysis.mpp.mark.set.UpdatableMarkSet
- remove(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
- remove(VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- removeAll(Collection<?>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- removeAndUpdateEnergy(VoxelizedMarksWithEnergy, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelDeathPixelized
- removeAndUpdateEnergy(MarksFromPartition, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelDeathPartition
- removeAndUpdateEnergy(T, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
- removeBelowThreshold(int) - Method in class org.anchoranalysis.math.histogram.Histogram
- removeClosestToUnitZ() - Method in class org.anchoranalysis.math.moment.ImageMoments
- removeEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
-
Remove an edge between two vertices.
- removeEdge(V, V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
Remove an edge between two vertices.
- RemoveExtensions - Class in org.anchoranalysis.plugin.io.bean.descriptivename
-
Removes extensions from the descriptive-name (but not from the file) AND only if the extension hasn't already been removed upstream.
- RemoveExtensions() - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
- RemoveExtensions(FileNamer) - Constructor for class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
- removeIfExists(FeatureList<FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
- removeIfExists(T) - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
- removeIntersectingVoxels(ObjectCollection, Dimensions, boolean) - Static method in class org.anchoranalysis.plugin.image.object.ObjectIntersectionRemover
- RemoveIntersectingVoxels - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
-
Considers all possible pairs of objects in a provider, and removes any intersecting pixels
- RemoveIntersectingVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
- removeLeft(int) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
-
Removes the first numToRemove pixels from the left
- RemoveMatching - Class in org.anchoranalysis.plugin.io.bean.provider.file
- RemoveMatching() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.RemoveMatching
- removeNonMatching(List<T>) - Method in class org.anchoranalysis.plugin.io.input.filter.FilterDescriptiveNameEqualsContains
- removeOrReplace(boolean, boolean, boolean) - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
-
Chops of one-side of keep, and one-side of merge
- RemoveOverlappingBoundingBoxes - Class in org.anchoranalysis.plugin.image.bean.box
-
Non-maxima suppression for axis-aligned bounding-boxes using an Intersection over Union score.
- RemoveOverlappingBoundingBoxes() - Constructor for class org.anchoranalysis.plugin.image.bean.box.RemoveOverlappingBoundingBoxes
- RemoveOverlappingObjects - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
Non-maxima suppression for object-masks using an Intersection over Union score.
- RemoveOverlappingObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.RemoveOverlappingObjects
- RemovePartition - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
- RemovePartition() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartition
- RemovePartitionAndThen<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.partition
- RemovePartitionAndThen() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartitionAndThen
- removePointsInMark(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- removeRight(int) - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
-
Removes the last numToRemove pixels from the right
- RemoveTouchingBorder - Class in org.anchoranalysis.plugin.image.bean.object.provider.filter
-
Considers all possible pairs of objects in a provider, and removes those that touch the border.
- RemoveTouchingBorder() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
- removeTouchingBorderXY(Extent) - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- RemoveTrailingDirectory - Class in org.anchoranalysis.plugin.quick.bean.file.path.derive
- RemoveTrailingDirectory() - Constructor for class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
- removeTwo(int, int) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- removeTwo(int, int, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- removeTwo(EnergySavedInd, int, int) - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
- removeTwo(MemoCollection, int, int, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- removeVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
-
Removes a vertex and any edges connected to it.
- removeVertex(V) - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
Removes a vertex and any edges connected to it.
- RemoveWhitespace - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.naming
-
Removes any whitespace characters from the path
- RemoveWhitespace() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.RemoveWhitespace
- repeat(int, CheckedRunnable<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate
-
Repeats an operation a number of times.
- Repeat - Class in org.anchoranalysis.bean.shared.color.scheme
- Repeat - Class in org.anchoranalysis.plugin.image.bean.segment.binary
- Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
- Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single
- Repeat - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position
- Repeat() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Repeat
- Repeat() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
- Repeat() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Repeat
- Repeat() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Repeat
- Repeat() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
- RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.channel.provider.slice
-
Creates a new channel with specific dimensions that repeatedly duplicates a slice from an existing channel
- RepeatSlice - Class in org.anchoranalysis.plugin.image.bean.mask.provider.slice
-
Creates a new mask with specific dimensions that repeatedly duplicates a slice from an existing mask
- RepeatSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
- RepeatSlice() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
- repeatUntil(int, CheckedBooleanSupplier<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate
-
Repeats an operation until a true value is returned.
- repeatWithIndex(int, CheckedIntConsumer<E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate
-
Repeats an operation a number of times, passing an increment index to
operationeach time. - Replace - Class in org.anchoranalysis.plugin.io.bean.path.derive
-
Generates a file-path by replacing all occurrences of a string-pattern with another
- Replace() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Replace
- replaceBy(BinaryVoxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.core.mask.Mask
- replaceError(ErrorNode) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
- replaceError(ErrorNode) - Method in class org.anchoranalysis.mpp.segment.kernel.KernelCalculationContext
- replaceError(ErrorNode) - Method in class org.anchoranalysis.mpp.segment.transformer.TransformationContext
- ReplaceInfinity<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
- ReplaceInfinity() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceInfinity
- replaceInput(T) - Method in class org.anchoranalysis.feature.session.SessionInputSequential
-
Replaces existing input with new input
- replaceInputManager(InputManager<?>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
- replaceInputManager(InputManager<?>) - Method in interface org.anchoranalysis.experiment.io.ReplaceInputManager
- replaceInputManager(InputManager<?>) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- replaceInputManager(InputManager<?>) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- ReplaceInputManager - Interface in org.anchoranalysis.experiment.io
-
Indicates and provides a mechanism that the
InputManagercan be replaced. - ReplaceNaN<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
- ReplaceNaN() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceNaN
- replaceOutputManager(OutputManager) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
- replaceOutputManager(OutputManager) - Method in interface org.anchoranalysis.experiment.io.ReplaceOutputManager
- replaceOutputManager(OutputManager) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- replaceOutputManager(OutputManager) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- ReplaceOutputManager - Interface in org.anchoranalysis.experiment.io
-
Indicates and provides a mechanism that the
OutputManagercan be replaced. - ReplacePropertyBeanFactory<T extends AnchorBean<T>> - Class in org.anchoranalysis.bean.xml.factory
-
Replaces a property (an XML element of attribute) on a bean before loading it
- ReplacePropertyBeanFactory(BeanInstanceMap) - Constructor for class org.anchoranalysis.bean.xml.factory.ReplacePropertyBeanFactory
- replaceSlice(int, VoxelBuffer<FloatBuffer>) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
- replaceSlice(int, VoxelBuffer<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
- replaceSlice(int, VoxelBuffer<UnsignedIntBuffer>) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
- replaceSlice(int, VoxelBuffer<UnsignedShortBuffer>) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
- replaceSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
- replaceSlice(int, VoxelBuffer<T>) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
- replaceSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.Voxels
-
Assigns a new buffer for a slice
- ReplaceStrategy<T extends FeatureInput> - Interface in org.anchoranalysis.feature.session.strategy.replace
- replaceTask(Task<T, S>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
- replaceTask(Task<T, S>) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
- replaceTask(Task<T, S>) - Method in interface org.anchoranalysis.experiment.io.ReplaceTask
- replaceTask(Task<U, S>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
- ReplaceTask<T extends InputFromManager,S> - Interface in org.anchoranalysis.experiment.io
-
/** Indicates and provides a mechanism that the
Taskcan be replaced. - ReplaceUnusualValue<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.replace
-
Calculates the underlying feature, but replaces the result with a constant if it happens to be an "unusual" value
- ReplaceUnusualValue() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.replace.ReplaceUnusualValue
- replaceVoxels(Voxels<?>) - Method in class org.anchoranalysis.image.core.channel.Channel
-
Assigns new voxels to replace the existing voxels
- replaceVoxels(Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Replaces the voxels in the object-mask.
- replaceVoxels(Voxels<T>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
Replaces the voxels in the box.
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFileMarksReporter
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
- reportBegin(FeedbackBeginParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- reportBegin(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
- reportBegin(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
- reportBegin(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
- reportBegin(FeedbackBeginParameters<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
- reportBegin(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
- reportEnd(FeedbackEndParameters<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- reportEnd(FeedbackEndParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
- reportEnd(FeedbackEndParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
- reportEnd(FeedbackEndParameters<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
- reportEnd(FeedbackEndParameters<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
- reportEnd(FeedbackEndParameters<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
- ReporterAggregate<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
- ReporterAggregate() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
- ReporterAggregate(double) - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterAggregate
- ReporterException - Exception in org.anchoranalysis.mpp.segment.optimization.feedback
- ReporterException(String) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.ReporterException
- ReporterException(Throwable) - Constructor for exception org.anchoranalysis.mpp.segment.optimization.feedback.ReporterException
- ReporterInterval<T> - Class in org.anchoranalysis.mpp.segment.bean.optimization.feedback
- ReporterInterval() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
- ReporterInterval(double) - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
- ReportFeature<T> - Class in org.anchoranalysis.io.output.bean
- ReportFeature() - Constructor for class org.anchoranalysis.io.output.bean.ReportFeature
- ReportFeatureEvaluator<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
- ReportFeatureEvaluator() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
- ReportFeatureForManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
- ReportFeatureForManifest() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifest
- ReportFeatureForManifestFileBase - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
- ReportFeatureForManifestFileBase() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
- ReportFeatureForMPP<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
- ReportFeatureForMPP() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForMPP
- ReportFeatureForSharedObjects - Class in org.anchoranalysis.mpp.io.bean.report.feature
- ReportFeatureForSharedObjects() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForSharedObjects
- ReportFeatureOnMark - Class in org.anchoranalysis.mpp.io.bean.report.feature
- ReportFeatureOnMark() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
- ReportFeatureOnMarks - Class in org.anchoranalysis.mpp.io.bean.report.feature
- ReportFeatureOnMarks() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
- ReportFeatureOnObject - Class in org.anchoranalysis.mpp.io.bean.report.feature
- ReportFeatureOnObject() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObject
- ReportFeatureOnObjectCollection - Class in org.anchoranalysis.mpp.io.bean.report.feature
- ReportFeatureOnObjectCollection() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectCollection
- ReportFeatureOnObjectsBase<T extends FeatureInput> - Class in org.anchoranalysis.mpp.io.bean.report.feature
- ReportFeatureOnObjectsBase() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
- ReportFeatureWrapError - Class in org.anchoranalysis.mpp.io.bean.report.feature
- ReportFeatureWrapError() - Constructor for class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
- reporting(int, StateReporter<T, U>, TransformationContext) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- Reporting<S> - Class in org.anchoranalysis.mpp.segment.optimization.step
-
Exposes data which is only needed by reporting tools
- reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
- reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
- reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
- reportItr(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- reportItr(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
- reportItr(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
- reportItr(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
- reportItr(Reporting<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
- reportItr(Reporting<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAccepted
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ConsoleAggregatedReporter
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterAggregated
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.CSVReporterBest
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.KernelIterDescriptionSerializerPeriodicReporter
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.Log4JReporter
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.OptimizationStepLogReporter
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFileMarksReporter
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- reportNewBest(Reporting<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
- reportNewBest(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
- reportNewBest(Reporting<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
- reportNewBest(Reporting<T>) - Method in interface org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackReceiver
- reportNewBest(Reporting<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.NullReporter
- RequireArguments - Class in org.anchoranalysis.experiment.bean.require
- RequireArguments() - Constructor for class org.anchoranalysis.experiment.bean.require.RequireArguments
- RequireDebugMode - Class in org.anchoranalysis.experiment.bean.require
- RequireDebugMode() - Constructor for class org.anchoranalysis.experiment.bean.require.RequireDebugMode
- RequireFeatureRelationThreshold - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
- RequireFeatureRelationThreshold() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
- reset() - Method in class org.anchoranalysis.core.cache.CachedSupplierBase
- reset() - Method in class org.anchoranalysis.math.arithmetic.RunningSum
-
Reset the sum and count to zero
- reset() - Method in class org.anchoranalysis.math.arithmetic.RunningSumCollection
-
Resets all items to zero.
- reset() - Method in class org.anchoranalysis.math.histogram.Histogram
- reset() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
- reset() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
- reset() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- reset() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.period.PeriodTriggerBank
- resetInd() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- ResettableCalculation - Interface in org.anchoranalysis.feature.calculate.cache
-
A calculation that be invalidated (resetted), removing any existing cached value.
- resizedXY(int, int, Interpolator) - Method in class org.anchoranalysis.image.voxel.extracter.Base
- resizedXY(int, int, Interpolator) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
-
Creates a new voxels that are a resized version of the current voxels (only in X and Y dimensions), interpolating as needed.
- resizeXY(int, int) - Method in class org.anchoranalysis.image.core.channel.Channel
- resizeXY(int, int, Interpolator) - Method in class org.anchoranalysis.image.core.channel.Channel
- resizeXY(Extent) - Method in class org.anchoranalysis.image.core.channel.Channel
- resizeXY(Extent, Interpolator) - Method in class org.anchoranalysis.image.core.channel.Channel
- resolution() - Method in class org.anchoranalysis.feature.energy.EnergyStack
-
The image-resolution asssociated with the energy-stack.
- resolution() - Method in class org.anchoranalysis.image.core.channel.Channel
- resolution() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
-
Resolution of voxels to physical measurements e.g.
- resolution() - Method in class org.anchoranalysis.image.core.mask.Mask
- resolution() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- resolution() - Method in class org.anchoranalysis.image.core.stack.Stack
- Resolution - Class in org.anchoranalysis.image.core.dimensions
-
The resolution of an image.
- Resolution() - Constructor for class org.anchoranalysis.image.core.dimensions.Resolution
- Resolution(double, double, double) - Constructor for class org.anchoranalysis.image.core.dimensions.Resolution
- Resolution(Tuple3d) - Constructor for class org.anchoranalysis.image.core.dimensions.Resolution
-
Constructs a resolution from a tuple.
- ResolutionAsXml - Class in org.anchoranalysis.plugin.io.xml
-
Reads and writes a metadata XML file specifying the image-resolution.
- resolutionRequired() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
- resolve(Optional<Resolution>, boolean) - Method in class org.anchoranalysis.mpp.bean.bound.Bound
- resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
- resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
- resolve(Optional<UnitConverter>, DirectionVector) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
- resolve(Optional<UnitConverter>, Point3d, Point3d) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
- resolve(Optional<UnitConverter>, Point3i, Point3i) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
- resolveArea(double, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
- resolveArea(double, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
-
Convert area into another unit representation
- ResolvedBound - Class in org.anchoranalysis.mpp.bean.bound
-
A bound resolved into pixel units
- ResolvedBound() - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
- ResolvedBound(double, double) - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
- ResolvedBound(ResolvedBound) - Constructor for class org.anchoranalysis.mpp.bean.bound.ResolvedBound
- ResolvedCalculation<S,T extends FeatureInput> - Class in org.anchoranalysis.feature.calculate.cache
-
Like a
FeatureCalculationbut has been resolved against a cache to reuse any existing identical instance. - ResolvedCalculation(FeatureCalculation<S, T>) - Constructor for class org.anchoranalysis.feature.calculate.cache.ResolvedCalculation
- ResolvedCalculationMap<S,T extends FeatureInput,U> - Class in org.anchoranalysis.feature.calculate.cache
-
A
FeatureCalculationMapthat has been resolved against a cache. - ResolvedCalculationMap(FeatureCalculationMap<S, T, U, FeatureCalculationException>) - Constructor for class org.anchoranalysis.feature.calculate.cache.ResolvedCalculationMap
-
Constructor
- resolveDistance(double, Optional<Resolution>, DirectionVector) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
-
Convert distance into another unit representation
- resolveFeatureIdentifier(String) - Method in interface org.anchoranalysis.feature.calculate.cache.FeatureSymbolCalculator
-
Due to scoping (different prefixes that can exist), an ID needs to be resolved to a unique-string before it can be passed to
calculateFeatureByIdentifier - resolveForAxis(Optional<UnitConverter>, AxisType) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
-
Resolves the distance in a direction aligned to a particular axis
- resolveName(String) - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
-
Adds a prefix before the name
- resolvePath(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
-
An absolute path to the prefix
- resolvePath(Path) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
-
Converts a relative-path to an absolute-path (relative to the file-path associated with this current bean)
- resolvePathToCurrentJar(String) - Method in class org.anchoranalysis.launcher.FilePathResolver
- resolvePathToCurrentJar(Path) - Method in class org.anchoranalysis.launcher.FilePathResolver
- resolver() - Method in interface org.anchoranalysis.feature.calculate.cache.SessionInput
-
Returns a resolver for calculations
- resolver() - Method in class org.anchoranalysis.feature.session.SessionInputSequential
- resolveTestPath(String) - Method in class org.anchoranalysis.test.TestLoader
-
Resolves a path to test-data (relative path to the test-data root) to an absolute path on the file system
- resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
- resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
- resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.UnitValueAreaOrVolume
-
Resolves a measurement of area/volume (in whatever units) to units corresponding to the image pixels/voxels.
- resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
- resolveToVoxels(Optional<UnitConverter>) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
- resolveVolume(double, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
- resolveVolume(double, Optional<Resolution>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
-
Convert volume into another unit representation
- resources() - Method in class org.anchoranalysis.launcher.config.LauncherConfig
-
Config for resources sued by the launcher
- ResourcesConfig - Class in org.anchoranalysis.launcher.config
- ResourcesConfig(ClassLoader, String, String, String, String) - Constructor for class org.anchoranalysis.launcher.config.ResourcesConfig
- ResultsVector - Class in org.anchoranalysis.feature.results
-
A vector of results from feature-calculations.
- ResultsVector(int) - Constructor for class org.anchoranalysis.feature.results.ResultsVector
- ResultsVectorList - Class in org.anchoranalysis.feature.results
-
A list of elements of type
ResultsVector. - ResultsVectorList() - Constructor for class org.anchoranalysis.feature.results.ResultsVectorList
- ResultsVectorList(ResultsVector) - Constructor for class org.anchoranalysis.feature.results.ResultsVectorList
- ResultsVectorTestUtilities - Class in org.anchoranalysis.test.feature.plugins
- ResultsVectorWithThumbnail - Class in org.anchoranalysis.plugin.image.task.feature
-
A results-vector with an optional thumbnail associated with it
- ResultsVectorWithThumbnail(ResultsVector) - Constructor for class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
- ResultsVectorWithThumbnail(ResultsVector, Optional<DisplayStack>) - Constructor for class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
- ResultsWriter - Class in org.anchoranalysis.feature.io.results
-
Feature calculation results that can be outputted in different ways.
- ResultsWriter(ResultsWriterMetadata, InputOutputContext) - Constructor for class org.anchoranalysis.feature.io.results.ResultsWriter
-
Creates for metadata and in a particular directory.
- ResultsWriterMetadata - Class in org.anchoranalysis.feature.io.results
-
Additional information needed for the outputs in
ResultsWriter. - ResultsWriterMetadata(LabelHeaders, FeatureNameList, ResultsWriterOutputNames) - Constructor for class org.anchoranalysis.feature.io.results.ResultsWriterMetadata
- ResultsWriterOutputNames - Class in org.anchoranalysis.feature.io.results
-
The customizable output names used by
ResultsWriter, which all follow a pattern based on a prefix. - ResultsWriterOutputNames() - Constructor for class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
-
Creates using default names, equivalent to a prefix of features.
- ResultsWriterOutputNames(String, boolean, boolean) - Constructor for class org.anchoranalysis.feature.io.results.ResultsWriterOutputNames
-
Creates output-names based upon a prefix.
- retainAll(Collection<?>) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- RetrieveDestinationFromDual - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
- RetrieveDestinationFromDual() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.RetrieveDestinationFromDual
- RetrieveDestinationFromVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
- RetrieveDestinationFromVoxelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.RetrieveDestinationFromVoxelized
- RetrieveSingleMarkOnly - Class in org.anchoranalysis.plugin.mpp.bean.provider.single
-
Retrieves a mark from a marks, assuming there is only one mark in a marks, otherwise throwing an exception
- RetrieveSingleMarkOnly() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.single.RetrieveSingleMarkOnly
- RetrieveSourceFromDual - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.dual
- RetrieveSourceFromDual() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.RetrieveSourceFromDual
- RetrieveSourceFromVoxelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
- RetrieveSourceFromVoxelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.RetrieveSourceFromVoxelized
- reuseByte(Voxels<UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory
-
Like
BinaryVoxelsFactory.reuseByte(org.anchoranalysis.image.voxel.Voxels<org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer>)but uses default binary-values for OFF (0) and ON (255). - reuseByte(Voxels<UnsignedByteBuffer>, BinaryValues) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory
-
Reuses an existing voxel-buffer (of type unsigned byte) as a binary-version which should have only two intensity-values representing OFF and ON
- reuseInt(Voxels<UnsignedIntBuffer>, BinaryValues) - Static method in class org.anchoranalysis.image.voxel.binary.BinaryVoxelsFactory
-
Reuses an existing voxel-buffer (of type unsigned int) as a binary-version which should have only two intensity-values representing OFF and ON
- ReuseSingletonStrategy<T extends FeatureInput> - Class in org.anchoranalysis.feature.session.strategy.replace
-
Always re-use a singleton SessionInput, invalidating it each time a new call occurs
- ReuseSingletonStrategy(CacheCreator) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.ReuseSingletonStrategy
-
Constructor with default means of creating a session-input
- ReuseSingletonStrategy(CacheCreator, FindChildStrategy) - Constructor for class org.anchoranalysis.feature.session.strategy.replace.ReuseSingletonStrategy
-
Constructor with custom means of creating a session-input
- reverse() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.combine.mergestrategy.MergeCandidate
- reversedList(List<Point3i>) - Static method in class org.anchoranalysis.image.core.outline.traverser.visited.ReverseUtilities
- reverseIterateArray(T[], CheckedConsumer<T, E>) - Static method in class org.anchoranalysis.core.functional.FunctionalIterate
-
Iterates through every element in an array in reverse order
- ReverseUtilities - Class in org.anchoranalysis.image.core.outline.traverser.visited
- rewind() - Method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Rewinds the buffer ala
ByteBuffer.rewind(). - RGB - Class in org.anchoranalysis.plugin.image.task.bean.format.convertstyle
-
Converts a set of channels to a single RGB-stack.
- RGB() - Constructor for class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGB
- rgbColor() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
- RGBColor - Class in org.anchoranalysis.core.color
- RGBColor() - Constructor for class org.anchoranalysis.core.color.RGBColor
- RGBColor(int) - Constructor for class org.anchoranalysis.core.color.RGBColor
- RGBColor(int, int, int) - Constructor for class org.anchoranalysis.core.color.RGBColor
- RGBColor(Color) - Constructor for class org.anchoranalysis.core.color.RGBColor
- RGBColorBean - Class in org.anchoranalysis.bean.shared.color
- RGBColorBean() - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean
- RGBColorBean(int, int, int) - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean
- RGBColorBean(Color) - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean
- RGBColorBean(RGBColor) - Constructor for class org.anchoranalysis.bean.shared.color.RGBColorBean
- RGBOutputUtils - Class in org.anchoranalysis.image.core.stack.rgb
- RGBStack - Class in org.anchoranalysis.image.core.stack.rgb
-
A stack with exactly three channels, respectively for Red, Green and Blue colors.
- RGBStack(Channel, Channel, Channel) - Constructor for class org.anchoranalysis.image.core.stack.rgb.RGBStack
- RGBStack(Dimensions, ChannelFactorySingleType) - Constructor for class org.anchoranalysis.image.core.stack.rgb.RGBStack
-
Creates a particularly-sized stack with all channels initialized to 0.
- RGBStack(Stack) - Constructor for class org.anchoranalysis.image.core.stack.rgb.RGBStack
-
Creates from an existing stack (which must have 1 or 3 channels).
- rightSize() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- rmv(int) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- rmvFromUpdatablePairList(ListUpdatableMarkSetCollection, Mark) - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- RootDirectory - Class in org.anchoranalysis.io.manifest.directory
- RootDirectory(Path) - Constructor for class org.anchoranalysis.io.manifest.directory.RootDirectory
- Rooted - Class in org.anchoranalysis.plugin.io.bean.filepath.prefixer
-
Prepend a 'root' before the file-path-prefix obtained from a delegate
- Rooted - Class in org.anchoranalysis.plugin.io.bean.path.derive
- Rooted - Class in org.anchoranalysis.plugin.io.bean.provider.file
-
Represents a set of files, with a different root depending on the operating-system and conditions.
- Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
- Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
- Rooted() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
- RootedFilePath - Class in org.anchoranalysis.plugin.io.bean.filepath
- RootedFilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
- RootedFilePathUtilities - Class in org.anchoranalysis.plugin.io.input.path
- RootFilePathRegEx - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
- RootFilePathRegEx() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
- rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixer
-
Provides a prefix that becomes the root-folder.
- rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
- rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
- rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
- rootFolderPrefix(String, FilePathPrefixerContext) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
- rootFolderPrefixAvoidResolve(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
-
Provides a prefix that becomes the root-folder.
- RootPath - Class in org.anchoranalysis.bean.shared.path
-
Defines a *root path* i.e.
- RootPath() - Constructor for class org.anchoranalysis.bean.shared.path.RootPath
- RootPathMap - Class in org.anchoranalysis.plugin.io.input.path
-
A collection of root-paths indexed by their name.
- RotatableBoundingBox - Class in org.anchoranalysis.mpp.mark.points
-
A two-dimensional bounding-box rotated at arbitrary angle in XY plane around a point.
- RotatableBoundingBox() - Constructor for class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
- rotate(double) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- RotateAngle2D - Class in org.anchoranalysis.spatial.rotation.factory
- RotateAngle2D(double) - Constructor for class org.anchoranalysis.spatial.rotation.factory.RotateAngle2D
- RotateAngle3D - Class in org.anchoranalysis.spatial.rotation.factory
- RotateAngle3D(double, double, double) - Constructor for class org.anchoranalysis.spatial.rotation.factory.RotateAngle3D
- RotateAxisAngle - Class in org.anchoranalysis.spatial.rotation.factory
- RotateAxisAngle(Vector3d, double) - Constructor for class org.anchoranalysis.spatial.rotation.factory.RotateAxisAngle
- rotatedPoint(double[]) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
- rotatedPoint(Point3d) - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
- rotateOneVectorOntoAnother(Vector3d, Vector3d) - Static method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
- RotationBounds - Class in org.anchoranalysis.mpp.bean.mark.bounds
- RotationBounds() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds
- RotationBounds2D - Class in org.anchoranalysis.mpp.bean.mark.bounds
-
Creates a randomly-generated orientation in 2D by uniformally sampling a scalar rotation angle
- RotationBounds2D() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
- RotationBounds3D - Class in org.anchoranalysis.mpp.bean.mark.bounds
-
Creates a randomly-generated orientation in 3D based upon Euler Angles
- RotationBounds3D() - Constructor for class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
- RotationMatrix - Class in org.anchoranalysis.spatial.rotation
-
A matrix that performs a rotation in Euclidean space.
- RotationMatrix(int) - Constructor for class org.anchoranalysis.spatial.rotation.RotationMatrix
- RotationMatrix(DoubleMatrix2D) - Constructor for class org.anchoranalysis.spatial.rotation.RotationMatrix
- RotationMatrixFactory - Class in org.anchoranalysis.spatial.rotation.factory
-
Base for classes that create a
RotationMatrixin different ways. - RotationMatrixFactory() - Constructor for class org.anchoranalysis.spatial.rotation.factory.RotationMatrixFactory
- RowLabels - Class in org.anchoranalysis.feature.io.csv
-
Labels for each row of feature-results in the outputted CSV row.
- RowLabels(String) - Constructor for class org.anchoranalysis.feature.io.csv.RowLabels
-
Creates with a single string as an identifier.
- RowLabels(Optional<String[]>, Optional<MultiName>) - Constructor for class org.anchoranalysis.feature.io.csv.RowLabels
- RTree<T> - Class in org.anchoranalysis.spatial.rtree
-
An R-Tree that contains items, each with an associated bounding-box.
- RTree(int) - Constructor for class org.anchoranalysis.spatial.rtree.RTree
-
Creates an empty R-Tree.
- run() - Method in interface org.anchoranalysis.core.functional.checked.CheckedRunnable
- runCommandLineApp(String[], LauncherConfig, Logger) - Static method in class org.anchoranalysis.launcher.Launch
-
Runs a command-line app, by parsing arguments
- runExperiment(String) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell
-
Runs an experiment identified by an XML found in the resources
- runExperiment(String, Optional<String>, Optional<String>) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell
-
Runs an experiment identified by an XML found in the resources
- runExperimentInTemporaryFolder(String, Optional<String>, Optional<String>, TemporaryFolder, String[]) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell
-
Creates a temporary-folder, copies data all data from the associated test-loader, and runs an experiment
- runExperimentInTemporaryFolder(String, TemporaryFolder) - Method in class org.anchoranalysis.test.experiment.launcher.ExperimentLauncherFromShell
-
Creates a temporary-folder, copies data all data from the associated test-loader, and runs an experiment
- RunningSum - Class in org.anchoranalysis.math.arithmetic
-
Mutable class that allows for incrementing jointly sum and count variables, so as to eventually calculate the mean.
- RunningSum() - Constructor for class org.anchoranalysis.math.arithmetic.RunningSum
- RunningSum(double, long) - Constructor for class org.anchoranalysis.math.arithmetic.RunningSum
- RunningSumCollection - Class in org.anchoranalysis.math.arithmetic
-
A collection of
RunningSumwhere an operation is executed on all objects in the collection. - RunningSumCollection(int) - Constructor for class org.anchoranalysis.math.arithmetic.RunningSumCollection
-
Constructor.
- RunningSumPoint - Class in org.anchoranalysis.spatial.point
-
A running sum for tracking points in each dimension
- RunningSumPoint() - Constructor for class org.anchoranalysis.spatial.point.RunningSumPoint
S
- sample(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- sample(RandomNumberGenerator) - Method in interface org.anchoranalysis.mpp.probmap.PointSampler
- sample(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.probmap.ProbMapObjects
- sample(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.probmap.ProbWeights
- sampleDoubleFromRange(double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
-
Generates a uniformly random floating-point number within a range from
0(exclusive) toendExclusive. - sampleDoubleFromRange(double, double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
-
Generates a uniformly random floating-point number within a range.
- sampleDoubleFromZeroCenteredRange(double) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
-
Generates a uniformly random floating-point number centered around
0ranging from[-halfWidth,+halfWidth](both exclusive). - sampleDoubleZeroAndOne() - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
-
Samples from a uniformly-distributed range between 0.0 (exclusive) and 1.0 (exclusive).
- sampleDoubleZeroAndOne() - Method in class org.anchoranalysis.core.random.RandomNumberGeneratorMersenne
- sampleFromAvailable(int) - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
-
Samples from the available marks
- sampleFromList(List<T>) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
-
Samples uniformly an item from a list
- sampleInteger(int) - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
-
Samples an integer uniformally between [0..maxVal)
- sampleIntFromRange(int) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
-
Generates a uniformly random discrete number within a range from 0 (inclusive) to
endExclusive. - sampleIntFromRange(int, int) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
-
Samples from a uniformly random discrete number within a range.
- sampleLongFromRange(long) - Method in interface org.anchoranalysis.core.random.RandomNumberGenerator
-
Generates a uniformly random discrete number within a range from 0 (inclusive) to
endExclusive. - sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- sampleRandomPairNonUniform(RandomNumberGenerator) - Method in class org.anchoranalysis.mpp.pair.RandomCollection
- SampleWithDirectory - Class in org.anchoranalysis.plugin.io.bean.provider.file
- SampleWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.SampleWithDirectory
- ScalarProposer - Class in org.anchoranalysis.mpp.bean.proposer
- ScalarProposer() - Constructor for class org.anchoranalysis.mpp.bean.proposer.ScalarProposer
- ScalarThreeDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
Like a
IntConsumerbut accepts three coordinates of a point as scalar arguments. - ScalarTwoDimensionalConsumer - Interface in org.anchoranalysis.spatial.point.consumer
-
Like a
IntConsumerbut accepts two coordinates of a point as scalar arguments. - scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.Bound
- scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
- scale(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
- scale(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- scale(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- scale(double) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
-
Objects are scaled in pre-rotated position.
- scale(double) - Method in class org.anchoranalysis.mpp.mark.Mark
-
Scales the mark in X and Y dimensions.
- scale(double) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
- scale(double) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- scale(double) - Method in class org.anchoranalysis.mpp.mark.points.PointList
- scale(double) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
- scale(double) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
- scale(double) - Method in class org.anchoranalysis.spatial.point.Point2d
- scale(double) - Method in class org.anchoranalysis.spatial.point.Point2f
- scale(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- scale(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- scale(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- scale(Channel, ScaleCalculator, Interpolator, MessageLogger) - Static method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
- scale(Mask, ScaleCalculator) - Static method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
- scale(ScaleFactor) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Produces a scaled-version of an object-mask.
- scale(ScaleFactor) - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
Scales the bounding-box, both the corner-point and the extent
- scale(ScaleFactor, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Produces a scaled-version of an object-mask.
- scale(ScaleFactor, Interpolator, Optional<Extent>) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
Creates a scaled-version (in XY dimensions only) of the current bounding-box
- scale(ScaleFactor, Extent) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
-
Scales the segmented-objects.
- scale(ScaleFactor, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
Scales the bounding-box corner-point, and assigns a new extent
- scale(ScaleFactor, Point3i) - Static method in class org.anchoranalysis.spatial.scale.ScaleFactorUtilities
-
Scales a point in XY (immutably)
- Scale - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Scales all the objects in the collection by a particular scale-factor.
- Scale - Class in org.anchoranalysis.plugin.mpp.bean.proposer.scalar
- Scale() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.Scale
- Scale() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
- scaleBy(double) - Method in class org.anchoranalysis.math.histogram.Histogram
- ScaleByMinMaxValue - Class in org.anchoranalysis.plugin.image.bean.channel.convert
-
Scales by compressing a certain range of values into the 8-bit signal
- ScaleByMinMaxValue() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
- ScaleByParams - Class in org.anchoranalysis.plugin.image.bean.channel.convert
-
Scales by compressing a certain range of values into the 8-bit signal
- ScaleByParams() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
- ScaleByTypeToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert
- ScaleByTypeToByte() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByTypeToByte
- ScaleCalculator - Class in org.anchoranalysis.image.bean.spatial
- ScaleCalculator() - Constructor for class org.anchoranalysis.image.bean.spatial.ScaleCalculator
- ScaleCalculatorConstant - Class in org.anchoranalysis.plugin.image.bean.scale
- ScaleCalculatorConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorConstant
- ScaleCalculatorInverted - Class in org.anchoranalysis.plugin.image.bean.scale
- ScaleCalculatorInverted() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorInverted
- ScaleCalculatorMinXYRes - Class in org.anchoranalysis.plugin.image.bean.scale
- ScaleCalculatorMinXYRes() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorMinXYRes
- ScaleCalculatorRelativeDimensions - Class in org.anchoranalysis.plugin.image.bean.scale
- ScaleCalculatorRelativeDimensions() - Constructor for class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
- scaleClipTo(ScaleFactor, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
Scales the bounding-box, both the corner-point and the extent - ensuring it remains inside a containing-extent
- ScaledElements<T> - Class in org.anchoranalysis.image.core.object.scale
-
A list of elements with an object-mask representation that have been scaled.
- ScaledMaskCreator - Interface in org.anchoranalysis.overlay.object.scaled
-
Creates a scaled version of a mask from a mark/object that is not scaled
- scaledObjectFor(T) - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements
-
Gets the scaled version of an element given the unscaled element.
- scaleElements(List<T>, ScaleFactor, Extent, AccessObjectMask<T>) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler
-
Scales every element in a list collectively, ensuring the results remain inside a particular region.
- ScaleFactor - Class in org.anchoranalysis.spatial.scale
-
What to scale x and y dimensions by
- ScaleFactor(double) - Constructor for class org.anchoranalysis.spatial.scale.ScaleFactor
- ScaleFactor(double, double) - Constructor for class org.anchoranalysis.spatial.scale.ScaleFactor
- ScaleFactorUtilities - Class in org.anchoranalysis.spatial.scale
- ScaleImage - Class in org.anchoranalysis.plugin.image.task.bean.scale
-
Task to scale an image.
- ScaleImage() - Constructor for class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- scaleObjects(ObjectCollection, ScaleFactor) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler
-
Scales every object-mask in a collection
- scaleObjects(ObjectCollection, ScaleFactor, Optional<UnaryOperator<ObjectMask>>, Optional<UnaryOperator<ObjectMask>>) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler
-
Scales every object-mask in a collection, allowing for additional manipulation before and after scaling.
- scaleObjects(ObjectCollection, ScaleFactor, Extent) - Static method in class org.anchoranalysis.image.core.object.scale.Scaler
-
Scales every object-mask in a collection, ensuring the results remain inside a particular region.
- scaleQuantity(double, int) - Static method in class org.anchoranalysis.spatial.scale.ScaleFactorUtilities
-
Multiplies a quantity (integer) by a scaling-factor, returning it as an integer
- Scaler - Class in org.anchoranalysis.image.core.object.scale
-
Scales object-masks (or other more generic elements) collectively to avoid undesired overlap.
- scaleRadii(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- ScaleToSize - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack
-
Create a thumbnail by scales an image to a particular size.
- ScaleToSize() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
- scaleX(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- scaleXY(double) - Method in class org.anchoranalysis.annotation.mark.DualMarksAnnotation
-
Scales the marks in the annotation in X and Y dimensions.
- scaleXY(double) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
- scaleXY(double) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
-
Scales the mark in X and Y dimensions.
- scaleXY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- scaleXY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- scaleXY(double, Extent) - Method in interface org.anchoranalysis.image.core.object.seed.Seed
- scaleXY(double, Extent) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- scaleXY(double, Extent) - Method in class org.anchoranalysis.image.core.object.seed.SeedObjectMask
- scaleXY(ScaleFactor) - Method in class org.anchoranalysis.image.core.channel.Channel
- scaleXY(ScaleFactor) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- scaleXY(ScaleFactor) - Method in class org.anchoranalysis.image.core.mask.Mask
- scaleXY(ScaleFactor, Interpolator) - Method in class org.anchoranalysis.image.core.channel.Channel
- ScaleXY - Class in org.anchoranalysis.plugin.image.bean.channel.provider.intensity
-
Scales the channel in the X and Y dimensions.
- ScaleXY - Class in org.anchoranalysis.plugin.image.bean.mask.provider.resize
-
Scales the mask in XY dimensions, but not in Z dimension.
- ScaleXY - Class in org.anchoranalysis.plugin.mpp.bean.provider.collection
- ScaleXY() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
- ScaleXY() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
- ScaleXY() - Constructor for class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
- scaleXYBy(ScaleFactor) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- scaleXYBy(ScaleFactor) - Method in class org.anchoranalysis.spatial.Extent
- scaleXYPoint(Point3d, double) - Static method in class org.anchoranalysis.mpp.mark.MarkWithPosition
- scaleXYTo(int, int) - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- scaleY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- sceneContains(Point2i) - Static method in class org.anchoranalysis.test.feature.plugins.objects.CircleObjectFixture
- ScoreObjects - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
- ScoreObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
- ScoreVoxels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.score
-
Assigns a score (a value indicating how probable something is) to each voxel
- ScoreVoxels() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- search(FeatureCalculation<S, T>) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculationResolver
-
Searches for an equivalent calculation to
calculation - search(FeatureCalculationMap<S, T, U, FeatureCalculationException>) - Method in interface org.anchoranalysis.feature.calculate.cache.CalculationResolver
-
Searches for an equivalent calculation to
calculation - second(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelBinary
- second(String) - Method in class org.anchoranalysis.io.output.enabled.multi.MultiLevelNot
- second(String) - Method in interface org.anchoranalysis.io.output.enabled.multi.MultiLevelOutputEnabled
-
A second-level of
OutputEnabledfor a particularoutputNameas used in first-level. - second(String) - Method in class org.anchoranalysis.io.output.enabled.OutputEnabledMutable
- second(String) - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
-
A
RecordedOutputsfor recording second-level outputs for a givenoutputNamefrom the first-level. - Second - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Evaluates the first-object in a pair only
- Second() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Second
- Second(Feature<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.Second
- SECOND - org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
- secondaryReport() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.StateReporter
- secondaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterIdentity
- secondaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
- secondaryReport() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
- secondEntries() - Method in class org.anchoranalysis.io.output.recorded.MultiLevelRecordedOutputs
-
All second-level recorded output entries.
- secondLevel(String) - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters
-
A writer that performs a second-level check on which outputs occur, but writes to the top-level directory.
- secondLevelOutputs(String, OutputEnabled) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
- secondPart() - Method in class org.anchoranalysis.feature.io.name.CombinedName
- secondPart() - Method in interface org.anchoranalysis.feature.io.name.MultiName
-
The second part of the name.
- secondPart() - Method in class org.anchoranalysis.feature.io.name.SimpleName
- Seed - Interface in org.anchoranalysis.image.core.object.seed
-
A seed provides an voxels that exclusively belong to a particular object, and can be used as a starting hint for segmentation.
- SeedCollection - Class in org.anchoranalysis.image.core.object.seed
- SeedCollection() - Constructor for class org.anchoranalysis.image.core.object.seed.SeedCollection
- SeedFinderException - Exception in org.anchoranalysis.image.experiment.seed
- SeedFinderException(String) - Constructor for exception org.anchoranalysis.image.experiment.seed.SeedFinderException
- SeedFinderException(Throwable) - Constructor for exception org.anchoranalysis.image.experiment.seed.SeedFinderException
- SeedObjectMask - Class in org.anchoranalysis.image.core.object.seed
- SeedObjectMask(ObjectMask) - Constructor for class org.anchoranalysis.image.core.object.seed.SeedObjectMask
- seek(int) - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
-
Seeks a particular slice
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
-
Segments a channel to produce an object-collection.
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
- segment(Channel, Optional<ObjectMask>, Optional<SeedCollection>, SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
- segment(NamedStacks, NamedProvider<ObjectCollection>, Optional<KeyValueParams>, InputOutputContext) - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
- segment(NamedStacks, NamedProvider<ObjectCollection>, Optional<KeyValueParams>, InputOutputContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
- segment(Stack) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentStackIntoObjectsPooled
-
Segments individually using a pool of size 1 just for one stack
- segment(Stack, ConcurrentModelPool<Net>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
- segment(Stack, ConcurrentModelPool<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentStackIntoObjectsPooled
-
Segments a stack to produce an object-collection.
- segment(Stack, ConcurrentModelPool<T>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentation
-
Performs a segmentation on voxels so that each voxel has an ON or OFF state after the operation.
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
- segment(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
- segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder
- segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderMask
- segmentAll(Voxels<?>, Voxels<?>, Voxels<UnsignedByteBuffer>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderWithoutMask
- SegmentationBean<T> - Class in org.anchoranalysis.image.bean.segment
-
Performs some kind of segmentation
- SegmentationBean() - Constructor for class org.anchoranalysis.image.bean.segment.SegmentationBean
- SegmentationFailedException - Exception in org.anchoranalysis.image.bean.nonbean.error
- SegmentationFailedException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.SegmentationFailedException
- SegmentationFailedException(String, Throwable) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.SegmentationFailedException
- SegmentationFailedException(Throwable) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.SegmentationFailedException
- SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment
-
Applies a
BinarySegmentationalgorithm to derive a mask from a channel - SegmentChannel - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
- SegmentChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
- SegmentChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
- SegmentChannelByObject - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Performs segmentation of a channel using each object in the upstream collection as a mask.
- SegmentChannelByObject() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
- SegmentChannelIntoObjects - Class in org.anchoranalysis.image.bean.segment.object
-
A base class for algorithms to segment a channel into one or more objects.
- SegmentChannelIntoObjects() - Constructor for class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects
- SegmentChannelIntoObjectsUnary - Class in org.anchoranalysis.image.bean.segment.object
-
A base-class for segmentations that takes another object-segmentation algorithm as a parameter.
- SegmentChannelIntoObjectsUnary() - Constructor for class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
- SegmentedObjects - Class in org.anchoranalysis.plugin.image.bean.object.segment.stack
-
Objects that are a result of an instance-segmentation.
- SegmentedObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
- SegmentedObjects(List<WithConfidence<ObjectMask>>) - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentedObjects
- segmentFromExistingSegmentation(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
- segmentFromExistingSegmentation(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Invert
- segmentFromExistingSegmentation(VoxelsWrapper, BinarySegmentationParameters, Optional<ObjectMask>, BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
- SegmentInstanceWithModel<T> - Class in org.anchoranalysis.plugin.image.task.bean.segment
-
Using a model-pool, performs instance segmentation on an image producing zero, one or more objects per image.
- SegmentInstanceWithModel() - Constructor for class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
- SegmentIntoMarks - Class in org.anchoranalysis.mpp.segment.bean
- SegmentIntoMarks() - Constructor for class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
- SegmentMarksFromImage - Class in org.anchoranalysis.plugin.mpp.experiment.bean.segment
-
Segments an image into a collection of
Marks. - SegmentMarksFromImage() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
- SegmentOnMaximumIntensityAndExpandInZ - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel
-
Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D segmentation.
- SegmentOnMaximumIntensityAndExpandInZ() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
- SegmentStack<T> - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Segments a stack into objects.
- SegmentStack() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
- SegmentStackIntoObjectsPooled<T> - Class in org.anchoranalysis.plugin.image.bean.object.segment.stack
-
A base class for algorithms to segment a stack into one or more objects - using a pool of models (e.g.
- SegmentStackIntoObjectsPooled() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.stack.SegmentStackIntoObjectsPooled
- SegmentText - Class in org.anchoranalysis.plugin.opencv.bean.object.segment.stack
-
Extracts text from a RGB image by using the EAST deep neural network model
- SegmentText() - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
- SegmentThresholdAboveMinBound - Class in org.anchoranalysis.plugin.mpp.bean.segment.binary
- SegmentThresholdAboveMinBound() - Constructor for class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
- SegmentWithMarkedPointProcess - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks
-
Segments a channel with marked pointed processes.
- SegmentWithMarkedPointProcess() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
- SegmentWithSeeds - Class in org.anchoranalysis.plugin.image.bean.object.provider.segment
-
Takes each object one-by-one from
objectsSource, and finds matching seeds fromobjectsSeeds - SegmentWithSeeds() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
- select(ExperimentExecutionArguments) - Method in class org.anchoranalysis.launcher.executor.selectparam.path.CustomManagerFromPath
- select(ExperimentExecutionArguments) - Method in interface org.anchoranalysis.launcher.executor.selectparam.SelectParam
-
Retrieves the parameter.
- select(ExperimentExecutionArguments) - Method in class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
- selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.All
- selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.FromStacks
-
Takes a stack-collection and extracts a set of references to particular channels (each with a name)
- selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
- selectChannels(ChannelSource, boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
- selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
- selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
- selectDelegate(StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
-
Selects a
StackWriterto use as a delegate. - SelectDimensions - Enum in org.anchoranalysis.image.voxel.object.morphological
- SelectDimensionsFactory - Class in org.anchoranalysis.image.voxel.object.morphological
- selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.KeyValueParamsGenerator
- selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.serialized.SerializedGenerator
- selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
- selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
- selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.tabular.CSVGenerator
- selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.text.StringGenerator
- selectFileExtension(OutputWriteSettings) - Method in class org.anchoranalysis.io.generator.xml.XMLGenerator
- SelectFromShared<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.list
-
Selects a number of features of shared-features matching against a regular-expression
- SelectFromShared() - Constructor for class org.anchoranalysis.feature.bean.list.SelectFromShared
- selectIndexToRmv(MarkCollection, ProposerContext) - Static method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath
- selective() - Method in class org.anchoranalysis.io.output.recorded.RecordingWriters
-
A writer that allows only certain selected output-names, and records the written output-names
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Repeat
- selectMarkFrom(MarkCollection, MarkFromCollectionProposer, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.UniformRandom
- selectMarkFrom(MarkCollection, ProposerContext) - Method in class org.anchoranalysis.mpp.bean.proposer.MarkFromCollectionProposer
- selectMarkFrom(MarkCollection, ProposerContext) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
- selectOutputEnabled(Optional<OutputEnabledRules>) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputsWithRules
-
Selects which
OutputEnabledRulesto employ. - SelectParam<T> - Interface in org.anchoranalysis.launcher.executor.selectparam
-
Different methods of selecting a object
Tthat is used as a parameter for an experiment. - SelectParamFactory - Class in org.anchoranalysis.launcher.executor.selectparam
-
Creates an appropriate
SelectParambased upon the options passed to the command-line. - SelectSlicesBase - Class in org.anchoranalysis.plugin.mpp.bean.region
- SelectSlicesBase() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
- SelectSlicesWithIndexBase - Class in org.anchoranalysis.plugin.mpp.bean.region
- SelectSlicesWithIndexBase() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
- separate(Collection<T>) - Method in class org.anchoranalysis.spatial.rtree.SpatiallySeparate
-
Splits the collection of objects into spatially separate clusters, without consuming all elements in
elements. - separateConsume(Set<T>) - Method in class org.anchoranalysis.spatial.rtree.SpatiallySeparate
-
Splits the collection of objects into spatially separate clusters, consuming all elements in
elements. - Sequence - Class in org.anchoranalysis.plugin.image.bean.segment.binary
-
Performs a sequence of succesive segmentations
- Sequence() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
- SequencedDirectory - Interface in org.anchoranalysis.io.manifest.directory.sequenced
- SequencedDirectoryDeserializer<T> - Class in org.anchoranalysis.io.manifest.directory.sequenced
-
Applies a deserializer to each file in a directory with a sequence of files.
- SequencedDirectoryDeserializer(SequencedDirectory, Deserializer<T>) - Constructor for class org.anchoranalysis.io.manifest.directory.sequenced.SequencedDirectoryDeserializer
-
Creates from a manifest-directory entry.
- SequenceInteger - Class in org.anchoranalysis.bean.permute.property
-
A sequence of integers.
- SequenceInteger() - Constructor for class org.anchoranalysis.bean.permute.property.SequenceInteger
- SequenceMemory - Class in org.anchoranalysis.io.generator.sequence
- SequenceMemory() - Constructor for class org.anchoranalysis.io.generator.sequence.SequenceMemory
- SequenceType<T> - Class in org.anchoranalysis.io.manifest.sequencetype
-
A sequence of elements (of type
T), which are mapped to a range of integer indices. - SequenceType() - Constructor for class org.anchoranalysis.io.manifest.sequencetype.SequenceType
- SequenceTypeException - Exception in org.anchoranalysis.io.manifest.sequencetype
- SequenceTypeException(Exception) - Constructor for exception org.anchoranalysis.io.manifest.sequencetype.SequenceTypeException
- SequenceTypeException(String) - Constructor for exception org.anchoranalysis.io.manifest.sequencetype.SequenceTypeException
- SequentialProcessor<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.processor
-
Executes jobs sequentially
- SequentialProcessor() - Constructor for class org.anchoranalysis.experiment.bean.processor.SequentialProcessor
- SequentialSession<T extends FeatureInput> - Class in org.anchoranalysis.feature.session
-
Calculates features with successively different parameters, taking care of caching etc.
- SerializedGenerator<T> - Class in org.anchoranalysis.io.generator.serialized
- SerializedGenerator(Optional<String>) - Constructor for class org.anchoranalysis.io.generator.serialized.SerializedGenerator
- SerializedObjectSupplier<T> - Interface in org.anchoranalysis.io.manifest.finder
-
Supplies a serialized-object (if it exists)
- serializeObjectToFile(T, Path) - Static method in class org.anchoranalysis.core.serialize.XStreamSerializer
-
Writes a file with a serialized representation of an object.
- SessionInput<T extends FeatureInput> - Interface in org.anchoranalysis.feature.calculate.cache
-
Encapsulates a feature-input in the context of a particular session.
- SessionInputSequential<T extends FeatureInput> - Class in org.anchoranalysis.feature.session
-
A feature-input that will be used in a
SequentialSession - SessionInputSequential(T, CacheCreator) - Constructor for class org.anchoranalysis.feature.session.SessionInputSequential
-
Constructor
- SessionInputSequential(T, CacheCreator, FindChildStrategy) - Constructor for class org.anchoranalysis.feature.session.SessionInputSequential
- set() - Method in class org.anchoranalysis.bean.StringSet
- set(int, double) - Method in class org.anchoranalysis.feature.results.ResultsVector
- set(int, ResultsVector) - Method in class org.anchoranalysis.feature.results.ResultsVector
- set(int, Seed) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- set(int, Mark) - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- set(int, UpdatableMarkSet) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- setAboveMaxValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
-
Constant to return if outside the range (above the maximum allowed)
- setAcceptNoResolution(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
- setAcceptOutsideScene(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
- setAdd(DefineAdderBean) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
- setAddCriteria(AddCriteria<T>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- setAdditionalBackgrounds(List<DerivePath>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
-
Additional background-stacks that are possible to use while annotating.
- setAdditionalChannels(List<ChannelEntry>) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
-
Additional channels other than the main one, which are located in the main raster file
- setAdditionalChannels(List<ChannelEntry>) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
Additional channels other than the main one, which are located in the main raster file
- setAdditionalPropertyPaths(StringSet) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
-
Additional property paths that are also changed, along with the main propertyPath *
- setAddName(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- setAddOne(boolean) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
- setAddSum(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBaseAddSum
-
Added to all gradients (so we can store negative gradients)
- setAdjacentChannels(List<AdjacentFile>) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
Channels that are located in a separate raster file adjacent to the main raster file
- setAggIntervalLog10(double) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.ReporterInterval
-
How many iterations before printing a new report? Encoded in log10.
- setAggregateTriggerBank(AggregateTriggerBank<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- setAll(EnergySavedAll) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
-
Certain features are stored for every object, so that we can reference them in our calculations for the 'all' component
- setAngleDegrees(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.AngleRotation
- setAngleRadians(double) - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- setAnnealScheme(AnnealScheme) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
- setAnnotations(AnnotationInputManager<NamedChannelsInputPart, T>) - Method in class org.anchoranalysis.plugin.annotation.bean.file.FromAnnotations
- setAnnotatorStrategy(S) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
- setAppendChannels(List<AppendStack>) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
Channels that are located in a separate raster file somewhere else in the project's structure
- setAppendCsv(AppendCsv) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
- setAppendCSV(DerivePath) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
- setAppendHistogram(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- setAppendObjects(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
-
Appends object-collections to the multi-input
- setAppendStack(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- setApplyResolution(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
-
Multiples the values by the x-resolution, if it exists.
- setArrange(ArrangeStack) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
- setArrange(ArrangeStackBean) - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
- setAsMemberFlag(byte, byte) - Static method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipUtilities
- setAsPercentage(boolean) - Method in class org.anchoranalysis.feature.bean.results.Quantile
-
If true, the quantile is interpreted as a percentage rather than a decimal
- setAssigner(AnnotationComparisonAssigner<T>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- setAssignMode(AssignMode<S, T, U>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
- setAvoidBulletOnFirst(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
-
Iff true no bullet is added for the very first-item in the list
- setAvoidDivideByZero(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
- setAvoidOverlappingObjects(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
-
If true, no overlapping objects are treated as pairs
- setAxis(String) - Method in class org.anchoranalysis.image.bean.spatial.direction.AxisAlignedUnitVector
-
Which axis the unit-vector will align with.
- setAxis(String) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
- setAxis(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientForAxis
-
Which axis? X=0, Y=1, Z=2
- setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.dimensions.ForSpecificAxis
- setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
- setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.boundingbox.BoundingBoxAlongAxisBase
- setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.GradientMeanForAxis
- setAxis(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.PrincipalAxisOrientation
-
Which axis to read from (x,y,z)
- setAxis(String) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
- setAxisColor(RGBColorBean) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- setAxisMax(double) - Method in class org.anchoranalysis.plot.AxisLimits
- setAxisMin(double) - Method in class org.anchoranalysis.plot.AxisLimits
- setBackground(AnnotationBackground) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
- setBackground(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
-
The background.
- setBackgroundChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
-
Uses only this channel (identified by an index in the stack) as the background, -1 disables.
- setBackgroundChannelName(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- setBackgroundChannelProvider(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
- setBackgroundColor(RGBColorBean) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- setBackgroundID(String) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
- setBackgroundStackMap(StringMap) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
-
If non-null, maps underlying stack-name to a background
- setBackgroundStackName(String) - Method in class org.anchoranalysis.mpp.segment.bean.SegmentIntoMarks
- setBeanExtension(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- setBeanExtension(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- setBelowMinValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
-
Constant to return if outside the range (below the minimum allowed)
- setBest(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
- setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
-
If true uses 8 neighborhood rather than 4 neighborhood etc.
- setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.DecomposeIntoConnectedComponents
-
if true, uses 8 neighborhood instead of 4, and similarly in 3d
- setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Dilate
- setBigNeighborhood(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
- setBinaryInputChannelID(String) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
-
The ID of the binary input mask that determines the region of the watershed
- setBinarySgmn(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.BinarySegmentByObject
- setBirthRepeats(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
- setBit0(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- setBit1(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- setBit2(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- setBit3(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- setBit4(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- setBit5(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- setBit6(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- setBit7(boolean) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- setBitsPerPixel(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceBitsPerPixel
- setBlockSize(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
-
The block-size as per OpenCV implementation (identical default-size)
- setBlockStride(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
-
The block-stride as per OpenCV implementation (identical default-size)
- setBlue(int) - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
- setBlue(int) - Method in class org.anchoranalysis.core.color.RGBColor
- setBlue(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
- setBorderWidth(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
-
Adds a border around each part of the montage
- setBoundCalculator(BoundCalculator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
- setBoundCalculator(BoundCalculator) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
- setBounds(RotationBounds) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.RandomOrientation
- setBoundsRatio(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
- setBoundType(BoundChangeEvent.BoundType) - Method in class org.anchoranalysis.core.index.bounded.BoundChangeEvent
- setBridgeMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
-
Used to match each input-object to an intermediary-object
- setBundleSize(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
- setBundleSize(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- setBySlices(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
- setCacheSize(int) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
-
Size of feature evaluation cache for featureEvaluatorMatch
- setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.image.bean.threshold.CalculateLevelOne
- setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
- setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
-
Method to calculate the level for a particular object.
- setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.GreaterThanThreshold
-
Calculates the level for the threshold
- setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.LevelFromHistogram
- setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
- setCalculateLevel(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
- setCalculateLevelElse(CalculateLevel) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
- setCellDefault(ArrangeStackBean) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
- setCells(List<Cell>) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
- setCellSize(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
-
The cell-size as per OpenCV implementation (identical default-size)
- setCenterPoint(Point3d) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- setChangeExisting(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertBase
-
If true, the existing channel can be changed.
- setChannel(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderUnary
- setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
- setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
- setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromChannelBase
- setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
- setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
- setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
- setChannel(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
-
A channel that is provided to the stack.
- setChannel1(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
- setChannel1(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
- setChannel2(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderBinary
- setChannel2(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
- setChannel3(ChannelProvider) - Method in class org.anchoranalysis.image.bean.provider.ChannelProviderTernary
- setChannelAssignFrom(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromChannel
- setChannelConversionStyle(ChannelConvertStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
-
To convert as RGB or independently or in another way
- setChannelConverter(ConvertChannelTo) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.Convert
- setChannelConverter(ConvertChannelTo) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
-
Optionally, how to convert from one bit-depth to another (scaling, clipping etc.)
- setChannelElse(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
- setChannelFilter(ChannelFilter) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
-
Optionally, includes only certain channels when converting.
- setChannelFirst(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
-
Index of first channel
- setChannelGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- setChannelID(String) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
-
The ID of the channel that provides the input to the filter
- setChannelIfVoxelZero(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.IfVoxelZero
-
If a pixel is zero in the input-channel, the output is formed from the corresponding pixel in this channel instead
- setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
- setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
- setChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
- setChannelIndex(int) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
-
If either stackAsChannel==true or we have specified additionalChannels this indicated which channel to use from the stack
- setChannelLookup(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.NormalizeDifferenceToMedian
- setChannelMap(ChannelMap) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
- setChannelMask(String) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
-
If defined, this is the name of channel used as a mask over the values which are fed into the histogram
- setChannelName(String) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
- setChannelName(String) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
-
By default all channels are converted into a stack.
- setChannelNum(Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
- setChannelSecond(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
-
Index of second channel
- setChannelsExtra(List<ChannelProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- setChannelsPerByteArray(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceChannelsPerByteArray
- setChannelThreshold(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
- setCheck(CheckMark) - Method in class org.anchoranalysis.plugin.mpp.bean.check.Not
- setCheckMark(CheckMark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
- setCheckMark(CheckMark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Check
- setCheckMark(CheckMark) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Check
- setCheckParsedFilePathBag(CheckParsedFilePathBag) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
-
Imposes a condition on each parsedFilePathBag which must be-fulfilled if a file is to be included
- setClassifierProvider(FeatureListProvider<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
- setClearOutsideMask(boolean) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
- setCol(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
- setCollapseFilename(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
- setCollectionID(String) - Method in class org.anchoranalysis.feature.bean.list.ParametersAsFeatures
- setCollectionID(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
- setColor(RGBColorBean) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromSingle
-
The single color to repeat.
- setColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
-
An optional color associated with the label when displayed via GUI
- setColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
- setColors(List<RGBColorBean>) - Method in class org.anchoranalysis.bean.shared.color.scheme.FromList
-
The list of colors to specify
- setColors(ColorScheme) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
-
The delegate that creates the (unshuffled) list.
- setColors(ColorScheme) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBaseWithGenerator
-
Colors to use for drawing objects
- setColorScheme(ColorScheme) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
- setColorsUnpaired(ColorScheme) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- setColorUnselectedObjects(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
-
Optionally outline the other (unselected for the thumbnail) objects in this particular color.
- setColumnDefinition(ColumnDefinition) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
-
Column definition for the CSVfiles
- setColumnFirstNumberPixels(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with the number of pixels for the first Object
- setColumnFirstPointX(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with X coordinate of point for the first Object
- setColumnFirstPointY(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with Y coordinate of point for the first Object
- setColumnFirstPointZ(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with Z coordinate of point for the first Object
- setColumnGroup(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
-
Name of CSV column used to group results (the same values, are outputted together)
- setColumnID(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
-
Name of CSV column with the file identifier
- setColumnNumPixels(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
-
Name of CSV column with the number of pixels for the first Object
- setColumnPointX(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
-
Name of CSV column with X coordinate of point for the first Object
- setColumnPointY(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
-
Name of CSV column with Y coordinate of point for the first Object
- setColumnPointZ(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
-
Name of CSV column with Z coordinate of point for the first Object
- setColumns(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
-
How many columns to use in the montage, or 0 to guess an approximately square output
- setColumnSecondNumberPixels(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with the number of pixels for the second Object
- setColumnSecondPointX(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with X coordinate of point for the first Object
- setColumnSecondPointY(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with Y coordinate of point for the first Object
- setColumnSecondPointZ(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
-
Name of CSV column with Z coordinate of point for the first Object
- setCombine(CombineObjectsForFeatures<T>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- setCommand(String) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
-
One of: open, close, fill, erode, dilate, skel, outline
- setComparerLeft(Comparer) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- setComparerRight(Comparer) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- setCondition(KeyValueCondition) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.IfParamEquals
- setCondition(KeyValueCondition) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfKeyValueCondition
- setConfidenceThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
-
The maximum difference in confidence for merging.
- setConstant(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
- setConstantBound(ResolvedBound) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.ConstantBoundGenerator
- setContains(String) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.DescriptiveNameContainsImageLabeller
- setContains(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
-
A descriptive-name must contain (case-sensitive) this string.
- setConvert(ConvertChannelToWithHistogram) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
- setConvexHull(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
-
If true, Reduces the set of points by applying a convex-hull operation
- setCopyFilesMethod(CopyFilesMethod) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- setCopyFilesNaming(CopyFilesNaming) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOne
- setCopyFilesNaming(CopyFilesNaming) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- setCountThreshold(int) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
-
If there are more than
countThresholdelements, usesummarizerGreaterThan, elsesummarizerElse. - setCov(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ObjectRadiusStandardDeviation
- setCreateMark(CreateMarkFromPoints) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.PointsFitter
- setCreateShort(boolean) - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
- setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
- setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
- setCreateShort(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
-
If True creates an unsigned short-image
- setCsvFilePath(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
- setCsvIgnoreZeros(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
-
Iff true, bins with zero-counts are not written as a row in the CSV file.
- setCurrentTemp(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
- setCustomName(String) - Method in class org.anchoranalysis.feature.bean.Feature
-
An optional additional name that be associated with the feature (defaults to an empty string)
- setDatasetName(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
The name of the experiment including version suffix
- setDatasetNameSubdirectory(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
If true the datasetName is appended as a subdirectory e.g.
- setDatasets(StringSet) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- setDatasets(StringSet) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- setDatasetSpecific(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- setDatasetSpecific(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- setDatasetSuffix(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
-
A suffix appended to the dataset name extracted from the reg exp
- setDatasetVersion(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
A version-suffix appended to the dataset name extracted from the reg exp
- setDay(boolean) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
-
If true, the current day (yyyy.MM.dd) is included in the output
- setDebug(boolean) - Method in class org.anchoranalysis.bean.shared.path.RootPath
-
If true this root is preferred, when executing a job in debugging mode
- setDebug(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
- setDefaultBehaviourString(Optional<String>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
-
If present, a string is printed in the description if the default-experiment is used, otherwise ignored.
- setDefaultColors(ColorScheme) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
-
The default color-scheme used for outputs, if no other scheme is specified.
- setDefine(Define) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
- setDefine(Define) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
- setDefine(DefineOutputterMPP) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
-
Defines entities (chanels, stacks etc.) that are derived from inputs and other entities.
- setDefine(DefineOutputterMPP) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
- setDefine(DefineOutputterMPP) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- setDefine(DefineOutputterMPPWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- setDefine(DefineOutputterMPPWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Adds definitions of stacks/objects etc.
- setDelaySizeAtEnd(int) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- setDelegate(ResolvedBound) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
- setDelimiter(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
- setDelta(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
- setDeltat(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
- setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.AnnotationMarksComparer
- setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MarksComparer
- setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
- setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.ObjectComparer
- setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.CollapseFileName
- setDerivePath(DerivePath) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
- setDestinationFolderPath(FilePath) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureForMPP
- setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromDimensionsBase
- setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.FromDimensionsBase
- setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
-
Dimensions to create new mask
- setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
- setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
- setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
- setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
- setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
- setDimensions(DimensionsProvider) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
- setDimensionsSource(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
- setDimensionsTarget(DimensionsProvider) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorRelativeDimensions
- setDirection(DirectionVectorBean) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.ConvertToPhysicalDistance
-
Direction of the distance being converted, defaults to a unit vector along the X-axis
- setDirection(VectorInDirection) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.direction.FeatureMarkDirection
- setDirectionVector(VectorInDirection) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
- setDirectory(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.HomeSubdirectory
-
A relative-path (to the user home directory) which is used as an output directory
- setDirectory(Path) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
- setDirectoryDistance(int) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
-
How many directories to recurse back from the current file to the Experiments/ directory
- setDisableDebugMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
- setDisableDebugMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
- setDisablePathModification(boolean) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationWriter
- setDistance(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
-
How many neighbors to include by distance (distance==1 implies all directly touching neighbors, distance==2 implies those touching the directly touching etc.)
- setDistance(MarkDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
- setDistanceMapProvider(ChannelProvider) - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
-
A distance map which can also be used for making decisions on merging
- setDistanceMax(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevel
- setDistanceTransformMultiplyBy(double) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
-
Multiplies the distance transform by this factor to make it more meaningful in a short
- setDistanceTransformSmoothSigmaMeters(double) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
-
If non-zero, a Gaussian blur is applied to the distance transform using the sigma in meters below
- setDistanceX(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
- setDistanceY(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
- setDistanceZ(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
- setDistanceZEndIfEmpty(UnitValueDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- setDivideByZeroValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.Divide
- setDivisor(double) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceDouble
-
Divide by
- setDivisor(int) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
-
What the identifier is divided by to find the modulo.
- setDo3D(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
- setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
- setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
-
Whether to perform the morphological dimensions in 3D or 2D
- setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
- setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
- setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
- setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
- setDo3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
- setDo3D(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
- setDummyMode(boolean) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- setDuplicate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting existing data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- setDuplicate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
-
If true the channel is duplicated after it is retrieved, to prevent overwriting exisiting data This is a shortcut to avoid embedding beans in a ChannelProviderDuplicate
- setElemAllCreator(FeatureListProvider<FeatureInputAllMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- setElement(T) - Method in class org.anchoranalysis.plugin.image.segment.WithConfidence
- setElemIndCreator(FeatureListProvider<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- setElemPairCreator(FeatureListProvider<FeatureInputPairMemo>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- setEmptyValue(double) - Method in class org.anchoranalysis.image.feature.bean.object.single.CenterOfGravity
- setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
- setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.ArbitraryInsidePoint
- setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
- setEmptyValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
- setEmptyValue(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
- setEnd(int) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
-
An index beyond which we cannot iterate (inclusive)
- setEnd(int) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
- setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
- setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
- setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
- setEnergyChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
- setEnergyChannelIndexCheck(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- setEnergyChannelIndexFail(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.NumberNeighboringVoxels
-
Index of which channel in the energy-stack to select
- setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
-
Index of which channel in the energy-stack to select
- setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.FeatureEnergyChannel
-
Index of channel to use in the energy-stack (0 is the first channel, 1 is second etc.)
- setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
- setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
-
The channel that that forms the histogram
- setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
-
The channel that that forms an object-mask with the bounding-box set to entire channel's dimensions
- setEnergyIndex(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
- setEnergyIndexGradient(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
- setEnergyIndexMask(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
-
A channel of the energyStack that is used as an additional mask using default byte values for ON and OFF
- setEnergyIndexMask(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
-
Optionally, index of another channel that masks the histogram.
- setEnergyIndexX(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
- setEnergyIndexY(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
- setEnergyIndexZ(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
- setEnergyParamsName(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
-
If non-empty, A keyValueParams is treated as part of the energyStack
- setEnergySchemeCreator(EnergySchemeCreator) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
- setEnergySchemeCreator(EnergySchemeCreator) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Creates an energy scheme that assigns an energy score to each collection of marks.
- setEnergyStack(Optional<EnergyStack>) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
- setEnergyStack(EnergyStack) - Method in class org.anchoranalysis.feature.input.FeatureInputEnergy
- setEnergyTotal(double) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
-
The pre-annealed total energy
- setEnergyTotal(double) - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- setEquals(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
-
A descriptive-name must be exactly equal to (case-sensitive) this string.
- setErodeAtBoundary(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mask.provider.ConvexHullBase
- setError(int, Exception) - Method in class org.anchoranalysis.feature.results.ResultsVector
- setErrorAll(Exception) - Method in class org.anchoranalysis.feature.results.ResultsVector
- setErrorDisconnectedObjects(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.RemoveIntersectingVoxels
-
If true, throws an error if there is a disconnected object after the erosion
- setErrorTree(DefaultTreeModel) - Method in class org.anchoranalysis.mpp.proposer.error.ProposerFailureDescription
- setExactDepth(int) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.DirectoryDepth
- setExceptionIfEmpty(boolean) - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
-
If true, then an exception is thrown if the histogram is empty, otherwise
is returned. - setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
-
Iff true, zero-valued voxels are excluded from the histogram
- setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanMaxSlice
- setExcludeZero(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
-
If true, zeros are excluded from considering in the histogram
- setExecutionTime(long) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- setExitBeforeOptimization(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Iff true the algorithm exits before optimization begins (useful for debugging).
- setExitWithMinima(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
-
If true, exits early and just returns the minima, without any further segmentation
- setExperimentIdentifier(ExperimentIdentifier) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
-
A name for the experiment.
- setExperimentIdentifier(ExperimentIdentifier) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- setExperimentType(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
-
A folder identifying the type of experiment (where the outputs are all put in the same directory
- setExperimentType(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
A folder identifying the type of experiment (where the outputs are all put in the same directory
- setExperimentType(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
- setExperimentType(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
-
The value of $1 (see comment above) in naming-structure.
- setExpression(String) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- setExtendInZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
-
Extends the objects in z-dimension (uses maximum intensity for the segmentation, but in all slices)
- setExtension(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStack
- setExtension(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendStackDirect
- setExtra(double) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
- setExtractScoreSize(ExtractScoreSize<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
- setExtractScoreSize(ExtractScoreSize<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
- setExtractScoreSizeReport(ExtractScoreSize<S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- setExtractScoreSizeState(ExtractScoreSize<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- setExtractWeight(ExtractWeightFromMark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
- setFactor(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
- setFactor(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
- setFactorHigh(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
- setFactorLow(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
- setFactorStdDev(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
- setFallback(ChannelConvertStyle) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.RGB
-
If a channel doesn't match an RGB pattern, this conversion-style can be used instead.
- setFallbackName(String) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
-
If there's no task-name, then this constant is used as a fallback name
- setFeature(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
-
Feature that calculates the score for an object.
- setFeature(Feature<FeatureInputPairMemo>) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
- setFeature(Feature<T>) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderDefine
- setFeature(Feature<T>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
-
The single feature that will be calculated (possibly repeatedly) in the session
- setFeature(Feature<T>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureBase
- setFeature(FeatureListElem<T>) - Method in class org.anchoranalysis.feature.bean.list.ListSequence
-
The list feature that is duplicated, and populated.
- setFeature(FeatureProvider<FeatureInputMark>) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
- setFeature(FeatureProvider<T>) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- setFeatureCondition(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
- setFeatureCondition(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
-
Calculates value for the condition - which is checked if it lies within a certain range
- setFeatureElse(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
- setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
- setFeatureEvaluator(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectCollectionProviderWithFeature
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
- setFeatureEvaluator(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeToIncreaseObjectFeature
- setFeatureEvaluator(FeatureEvaluator<T>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
- setFeatureEvaluatorMatch(FeatureEvaluator<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
- setFeatureEvaluatorMerge(FeatureEvaluator<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
- setFeatureEvaluatorThreshold(FeatureEvaluator<FeatureInputNull>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
-
Allows merge only if the feature-value satisfies a relation to this threshold
- setFeatureListRef(String) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
- setFeatures(List<NamedBean<FeatureListProvider<FeatureInputSingleObject>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
-
Features to calculate for objects in the features output.
- setFeatures(List<NamedBean<FeatureListProvider<U>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
-
The features to be exported (after possibly some manipulation or augmentation)
- setFeatures(List<FeatureProvider<T>>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureListEvaluator
-
A list of providers, combined together to form a list of features, to be calculated in a session
- setFeaturesAggregate(List<NamedBean<FeatureListProvider<FeatureInputResults>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
-
Features applied to each group to aggregate values (takes FeatureResultsVectorCollection)
- setFeaturesImage(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
-
Additional features that only depend on the image, so do not need to be replicated for every object.
- setFeaturesPair(List<NamedBean<FeatureListProvider<FeatureInputPairObjects>>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
-
Additional features that are processed on the pair of images (i.e.
- setFeatureTables(List<OutputFeatureTable>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.define.Develop
-
Specifies a feature-table that can also be outputted.
- setFeedbackReceiver(FeedbackReceiverBean<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Processes feedback from the segmentation algorithm for outputting / debugging.
- setFeedbackReceiver(FeedbackReceiverBean<T>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
- setFileFilter(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
Files to search for
- setFileId(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendCsv
-
Unique identifier for the stack, object-mask-collection etc.
- setFileId(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathBaseAppendToManagerWithFileID
-
Unique identifier for the stack, object-mask-collection etc.
- setFileInput(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
-
A string indicating the input file(s)
- setFileInput(InputManager<FileInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
- setFileInput(InputManager<FileInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
- setFileInput(NamedFiles) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- setFileName(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
- setFilenamePrefix(String) - Method in class org.anchoranalysis.io.output.path.prefixer.DirectoryWithPrefix
- setFilePath(String) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
- setFilePath(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromSerializedMarks
- setFilePath(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.FromSerializedObject
- setFilePath(Path) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
- setFilePathParser(FilePathParser) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- setFilePathParser(FilePathParser) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
- setFilePathPrefixer(PathPrefixer) - Method in class org.anchoranalysis.io.output.bean.OutputManager
-
Determines a prefix to use when outputting a file based upon an input-path.
- setFilePathPrefixer(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.LastDirectoryAsPrefix
- setFilePathPrefixer(PathPrefixerAvoidResolve) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
- setFilePathProviderSVM(FilePathProvider) - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
- setFilePrefix(String) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- setFilesProvider(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- setFilesProvider(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
-
The files to use as inputs.
- setFilesProvider(FilesProviderWithDirectory) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
- setFilesProvider(FilesProviderWithDirectory) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
A path to the main channel of each file
- setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfObjectFilter
- setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
- setFilter(ObjectFilter) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Filter
- setFilter(ImageLabeller<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
- setFilterFilesCsv(MatchedAppendCsv) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
If set, a CSV is read with two columns: the names of images and a
- setFindMaxima(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
-
If true, the maxima of the score is searched for.
- setFindOutlinePixelAngle(FindPointOnOutline) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
- setFirst(boolean) - Method in class org.anchoranalysis.mpp.feature.bean.energy.element.AsSingle
-
Iff true, first object is used, otherwise the second
- setFirst(StringSet) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
-
Output-names in the first-level.
- setFirst(StateTransformerBean<S, U>) - Method in class org.anchoranalysis.mpp.segment.transformer.Compose
-
First transformation from
StoU - setFirstLineHeaders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- setFixRandomSeed(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Iff true uses a constant seed for the random-number-generator (useful for debugging).
- setFlatten(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
-
If true, any 3D mask is flattened in the z-dimension (maximum intensity projection) to make it 2D
- setFlatten(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
-
If true, objects and the background are flattened in the z dimension (via maximum intensity projection), so that a 2D image is produced
- setFolderDataset(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- setFolderOutput(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- setForceBinary(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- setForceChangeBytes(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
-
If true, rather than modifying the binary-values (an index) bytes are modified in the buffer to reflect the existing binary-values.
- setForceDetailedLogging(boolean) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
-
Whether more detailed log-messages around each experiment occur.
- setForceEagerEvaluation(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- setForceReader(String) - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
-
If non-empty forces usage of a particular bioformats plugin
- setForceRGB(boolean) - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
-
If set, ensures every stack is converted into 3 channels
- setForwardDirectionOnly(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- setFrom3i(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
-
A sorted-set of three-dimensional integer points from the entire object-mask
- setFromOutline(ObjectMask) - Static method in class org.anchoranalysis.image.core.points.PointsFromObject
- setGaussian(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
-
If true, the Gaussian filter is included
- setGaussianSigmaMeters(double) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
- setGradient(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- setGraphColorScheme(PlotColorScheme) - Method in class org.anchoranalysis.plot.index.PlotIndexBase
- setGrayscaleReconstruction(GrayscaleReconstructionByErosion) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.minima.MinimaImpositionGrayscaleReconstruction
- setGreen(int) - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
- setGreen(int) - Method in class org.anchoranalysis.core.color.RGBColor
- setGreen(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
- setGroup(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
-
Specifies a group for the label (similar labels that are displayed together)
- setGroup(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
- setGroup(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendHistogram
- setGroup(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
-
If non-null this file-path is used to determine the group of the file If null, no group is included.
- setGroup(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
-
If defined, translates a file-path into a group.
- setGroupNum(int) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
- setHeight(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
- setHighestTwoRadiiOnly(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
- setHistogram(HistogramProvider) - Method in class org.anchoranalysis.image.bean.provider.HistogramProviderUnary
- setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.convert.ConvertWithHistogram
-
If set, a histogram used in conversion to describe input intensities (across perhaps multiple images).
- setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
-
An optional histogram of voxel intensity values which can be used by
segment - setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
-
The histogram to plot.
- setHistogram(HistogramProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromHistogram
-
If non-null, a histogram is extracted from this provider rather than the histogram from the inputted CSV.
- setHistogramChannelIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.CalculateLevelBase
- setHistogramIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- setHistogramsExtra(List<HistogramProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- setHistogramsOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
-
Deprecated.What's allowed or not when outputting histograms
- setHorizontalAlign(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
- setId(int) - Method in class org.anchoranalysis.mpp.mark.Mark
- setId(int) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
- setId(String) - Method in class org.anchoranalysis.bean.shared.params.keyvalue.KeyValueParamsProviderReference
- setId(String) - Method in class org.anchoranalysis.feature.bean.operator.Reference
- setId(String) - Method in class org.anchoranalysis.feature.bean.provider.FeatureProviderReference
- setId(String) - Method in class org.anchoranalysis.feature.bean.results.StatisticForFeature
- setId(String) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationReference
- setId(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.Reference
- setId(String) - Method in class org.anchoranalysis.plugin.image.bean.dimensions.provider.FromChannel
- setId(String) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.Reference
- setId(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Reference
- setId(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Reference
- setId(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
- setId(String) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Reference
- setId(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
-
ID for the particular object-collection
- setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsReference
- setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerReference
- setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MarkMergeProposerReference
- setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkSplitProposerReference
- setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.Reference
- setId(String) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ReferenceOrEmpty
- setId(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
- setId(String) - Method in class org.anchoranalysis.plugin.points.bean.fitter.Reference
- setId(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
-
Translates an input file name to a unique ID
- setIdentifierSuffix(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- setIdentifierSuffix(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- setIdGenerator(DerivePath) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
- setIdGetter(IdentifierGetter<T>) - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
- setIgnoreAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
- setIgnoreCase(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
- setIgnoreContains(String) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
-
If non-empty any stackNames (after map) containing a certain string will be ignored
- setIgnoreFileNotFoundAppend(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- setIgnoreFittingFailure(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
-
If true, if too few points exist to make a mark, or otherwise a fitting errors, it is simply not included (with only a log error) If false, an exception is thrown
- setIgnoreHidden(boolean) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.path.FilePathPattern
- setIgnoreHigherSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
- setIgnoreLowerSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
- setIgnoreMissingChannel(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.format.convertstyle.IndependentChannels
-
Iff true and we cannot find a channel in the file, we ignore it and carry on
- setIgnoreNaN(boolean) - Method in class org.anchoranalysis.feature.bean.operator.Sum
-
If true, we ignore any NaN values.
- setIgnoreNoObjects(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
-
If true, then the outputs (outline, mask, image etc.) are not written for images that produce no objects.
- setIgnoreRangeAxisOutside(boolean) - Method in class org.anchoranalysis.plot.index.LinePlot
- setIgnoreZero(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.RatioNonMode
- setImageLabeller(ImageLabeller<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
-
Maps a label to an image
- setImgChannelMapCreator(ChannelMap) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- setIncludeFeatureNames(boolean) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
-
If true, the names of the imageFeatures are taken as a combination of the namedItem and the actual features
- setIncludeFileName(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
- setIncludeFirst(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
-
Include features for the First-object of the pair
- setIncludeFolders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
-
If false, the folders are ignored, and only the file-name is used in the output
- setIncludeMerged(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
-
Include features for the Merged-object of the pair
- setIncludeSecond(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
-
Include features for the Second-object of the pair
- setIncludeShell(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
- setIncludeZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.NotTouchingSceneBorder
- setIncrement(int) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
-
Size of step to use when incrementing
- setIncrementDegrees(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtent
- setIncrementDegrees(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
- setIndex(int) - Method in interface org.anchoranalysis.core.index.IndexSetter
- setIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.AtIndex
- setIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
-
Index in z-dimension of slice to extract
- setIndex(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
-
Specifies which principal-axis to use for calculations (0=largest eigenvalue, 1=second-largest eigenvalue etc.)
- setIndex(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- setIndex(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.OrderedRadius
- setIndex(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
- setIndex(int) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
-
Which index to return from the HOG descriptor
- setIndex(int, double) - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
-
Sets an element of the vector by the index of its position, index=0 is the X-element, index=1 is the Y-element etc.
- setIndexNonZero(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
- setInitContext(OptimizationContext) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- setInitialKernel(Kernel<T>) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- setInnerCoreDistance(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- setInPathPrefix(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.DirectoryStructure
- setInput(InputManager<? extends ProvidesStackInput>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- setInput(InputManager<NamedChannelsInput>) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
- setInput(InputManager<NamedChannelsInputPart>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- setInput(InputManager<T>) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationInputManager
- setInput(InputManager<T>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
-
The input-manager to specify where/which/how necessary inputs for the experiment occur.
- setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
- setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
- setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
- setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterDescriptiveName
- setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterIfDebug
- setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
- setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.Shuffle
- setInput(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
- setInput(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
- setInput(MultiInputManager) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.FromCSVInputManager
- setInputDebug(InputManager<T>) - Method in class org.anchoranalysis.plugin.io.bean.input.BranchIfDebug
- setInputDirectory(Optional<Path>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
- setInputFilterExtensions(Optional<Set<String>>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
-
If defined, a set of extension filters that can be applied on inputDirectory
- setInputFilterGlob(Optional<String>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
-
If non-null, a glob that is applied on inputDirectory
- setInputName(String) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- setInputName(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- setInputName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
- setInputPaths(List<Path>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
- setInputPointShift(float) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
- setIntensity(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- setInterpolate(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
- setInterpolator(InterpolatorBean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
- setInterpolator(InterpolatorBean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
-
Interpolator used when scaling the background
- setInterpolator(InterpolatorBean) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
- setInverse(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.IntersectsWithContainer
- setInverse(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
-
Iff true, calculates instead on the inverse of the object-mask (what's left when the shell is removed)
- setInverseMask(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
- setInvert(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
- setInvert(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
- setInvert(boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.EnsureRegExMatch
-
Iff true, then a file is rejected if regEx matches and vice-versa (opposite to normal behaviour)
- setInvertDecisionValue(boolean) - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
- setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
- setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.Intensity
-
Feature to apply to the histogram
- setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.intensity.Intensity
-
Feature to apply to the histogram
- setItem(Feature<FeatureInputHistogram>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
-
Feature to apply to the histogram
- setItem(Feature<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
- setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
- setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.DerivedObject
- setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.FeatureSingleObjectFromShared
- setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.AsObjectMask
- setItem(Feature<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
- setItem(Feature<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.CoefficientOfVarianceFromAll
- setItem(Feature<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.all.MeanFromAll
- setItem(Feature<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoOne
- setItem(Feature<S>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureUnary
- setItem(Feature<T>) - Method in class org.anchoranalysis.feature.bean.list.DefineSingle
- setItem(FeatureListProvider<FeatureInput>) - Method in class org.anchoranalysis.feature.bean.list.PrependName
- setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
- setItem(FeatureListProvider<FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
-
For each feature in the list, a corresponding "aggregate" feature is created in the output list
- setItem(FeaturePairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
- setItem(VoxelScore) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
- setItem(DerivePath) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
- setItem(ReportFeature<MPPInitParams>) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
- setItem(T) - Method in class org.anchoranalysis.bean.NamedBean
-
The item that is to be named (i.e.
- setItem(T, int) - Method in class org.anchoranalysis.core.index.bounded.SingleContainer
- setItem1(Feature<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
- setItem2(Feature<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureDoubleElem
- setItemMean(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
- setItemProportionate(Feature<FeatureInputSingleMemo>) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeatureAsIndividualProportionate
- setItemStdDev(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
- setIterations(int) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
- setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
- setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.ObjectCollectionProviderMorphological
- setIterations(int) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Repeat
-
The maximum number of iterations.
- setIterations(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Erode
- setIterations(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.NumberRemovedVoxelsAfterClosing
- setIterations(int) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.MorphologicalOperation
-
iterations for erode, dilate, open, close
- setIterations(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
- setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.Intersection
-
The number of dilations and erosions to apply to determine if two objects intersect
- setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.IntensityMeanShellBase
-
The number of dilations and erosions to apply and whether to do in the Z dimension
- setIterations(MorphologicalIterations) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
-
The number of dilations and erosions to apply and whether to do in the Z dimension
- setIterationsDilation(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
-
Number of times to perform morphological dilation
- setIterationsErosion(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
-
Number of times to perform morphological erosion
- setJobNumber(int) - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
- setJobShortName(String) - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
- setKappa(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
- setKeepEntireImage(boolean) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
-
If true, rather than writing out a bounding-box around the object-mask, the entire image is written
- setKeepExtremes(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
- setKeepProcessorsFree(int) - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
-
How many processors to avoid using for the tasks.
- setKeepProcessorsFree(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
-
How many processors to avoid using for the tasks.
- setKeepZ(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
-
Keep the z-resolution if it is already defined
- setKernel(Kernel<T>) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
- setKernel(Kernel<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
- setKernelFactoryList(WeightedKernelList<?>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- setKernelHalfWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Median
-
Kernel will be a square kernel of size
(2*kernelHalfWidth+1)x(2*kernelHalfWidth+1) - setKernelNegative(KernelPosNeg<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
- setKernelPositive(KernelPosNeg<T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
- setKernelProposer(KernelProposer<VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Proposes kernel-changes during iterations of hte marked-point-processes.
- setKernelStateBridge(KernelStateBridge<U, T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
- setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
- setKey(String) - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
- setKey(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.ParamFromCollection
- setKey(String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
- setKeyGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- setKeyLower(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
- setKeyMean(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
- setKeyPrefix(String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
-
Prefix prepended to key
- setKeyRequired(boolean) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- setKeyStdDev(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
- setKeySuffix(String) - Method in class org.anchoranalysis.plugin.operator.feature.bean.Param
- setKeyUpper(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
- setKeyValueParamsID(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromParams
- setKeyValueParamsID(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
-
If non-empty, the identifier of a key-value-params collection that is passed to the segmentation procedure.
- setLabel(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
-
If true a label is added beside every image showing the slice index
- setLabels(List<AnnotationLabel>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
- setLevel(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Constant
- setLine(String[]) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
- setList(List<DefineAdderBean>) - Method in class org.anchoranalysis.bean.define.adder.Concatenate
- setList(List<NamedBean<FeatureListProvider<T>>>) - Method in class org.anchoranalysis.feature.bean.list.DefinedNamed
- setList(List<NamedBean<FromStack>>) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
- setList(List<Provider<Stack>>) - Method in class org.anchoranalysis.image.bean.provider.stack.ArrangeRaster
- setList(List<RegEx>) - Method in class org.anchoranalysis.bean.shared.regex.RegExList
- setList(List<StringMapItem>) - Method in class org.anchoranalysis.bean.shared.StringMap
- setList(List<LoggingDestination>) - Method in class org.anchoranalysis.experiment.bean.log.ToMultiple
-
The list of loggers to log to
- setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.Define
- setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- setList(List<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
- setList(List<ObjectFilter>) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.combine.ObjectFilterCombine
-
A list of other filters from which the sub-classes implement filtering behaviour.
- setList(List<ColorProvider>) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.Concatenate
- setList(List<ObjectCollectionProvider>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Concatenate
- setList(List<BinarySegmentation>) - Method in class org.anchoranalysis.plugin.image.bean.segment.binary.Sequence
-
A list of binary-segmentations that are applied successively (the output of the predecessor becomes the input of the sucecssor)
- setList(List<CalculateLevel>) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelListBase
- setList(List<ProviderAsStack>) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.Concatenate
- setList(List<ChannelEntry>) - Method in class org.anchoranalysis.plugin.io.bean.channel.map.FromEntries
- setList(List<FilesProvider>) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Combine
- setList(List<InputManager<T>>) - Method in class org.anchoranalysis.plugin.io.bean.input.Concatenate
- setList(List<MarkProposer>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerFromList
- setList(List<RegionMembership>) - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMap
- setList(List<AddCriteriaPair>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.AddCriteriaOr
- setList(List<CheckMark>) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
- setList(List<TerminationCondition>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
- setList(List<FeedbackReceiver<T>>) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverList
- setList(List<Summarizer<T>>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
- setList(List<VisitScheduler>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
- setList(List<VisitScheduler>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
- setList(FeatureList<T>) - Method in class org.anchoranalysis.feature.bean.operator.FeatureListElem
- setListAdditionalChannelProviders(List<ChannelProvider>) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
- setListAppend(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- setListAppend(List<FilePathBaseAppendToManager>) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
-
Additional entities that are appended to the multi-input
- setListAppendFilePath(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- setListAppendKeyValueParams(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- setListAppendMarks(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- setListAppendMarksFromAnnotation(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- setListAppendMarksFromAnnotationAcceptedOnly(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- setListAppendMarksFromAnnotationRejectedOnly(List<NamedBean<DerivePath>>) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- setListComparers(List<NamedBean<Comparer>>) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
- setListFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
- setListImageFeatures(List<NamedBean<FeatureListProvider<FeatureInputStack>>>) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- setListReportFeatures(List<ReportFeature<DeserializedManifest>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeaturesFromManifest
- setListReportFeatures(List<ReportFeatureForSharedObjects>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.task.ExportReportFeatures
- setListStackProvider(List<NamedBean<StackProvider>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- setListStackProviderMIP(List<NamedBean<StackProvider>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
-
The channels we extract the object-masks from - all assumed to be of same dimension
- setLog(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf
-
The logger to use if conditions are fulfilled
- setLog(LoggingDestination) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- setLogExperiment(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
-
Where log messages that do not pertain to a specific job (input) appear.
- setLogExperimentPath(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
-
Relative path to a logger for the experiment in gneeral
- setLoggerTaskCreator(LoggingDestination) - Method in class org.anchoranalysis.experiment.task.ParametersExperiment
- setLogPath(boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
-
if true, the pathIn and pathOut are logged.
- setLogTask(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
-
Where log messages that do pertain to a specific job (input) appear.
- setLogTaskPath(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
-
Relative path to a logger for a specific task
- setLookup(StringList) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
- setMainChannelIndex(int) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
Index of the mainChannel
- setMainChannelName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
The name of the channel provided by the rasters in file Provider
- setManifestDescriptionFunction(String) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
- setManifestDeserializer(ManifestDeserializer) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
- setManifestExperimentInputFileSet(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
- setManifestFunction(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.ObjectSerializerPeriodicReporter
- setManifestFunction(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- setManifestInputFileSet(FilesProvider) - Method in class org.anchoranalysis.plugin.io.bean.input.manifest.CoupledManifestsInputManager
- setMap(StringMap) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageLabellerStringMap
- setMarkBounds(MarkBounds) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.MarkBoundsDefine
- setMarkBounds(MarkBounds) - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
- setMarkEvaluator(NamedBean<MarkEvaluator>) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
-
A mark-evaluator that is added to the GUI to support this annotation
- setMarkFactory(MarkFactory) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
- setMarkFactory(MarkWithIdentifierFactory) - Method in class org.anchoranalysis.mpp.feature.bean.mark.MarkEvaluator
- setMarkFactory(MarkWithIdentifierFactory) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
Creates a new mark, before perhaps further manipulations by a kernel.
- setMarkFromMarksProposer(MarkFromCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
- setMarkProposer(String) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
-
Name of the
MarkProposerto use. - setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
- setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
- setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
- setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
- setMarkProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
- setMarkProposerAdditionalBirth(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- setMarkProvider(Provider<Optional<Mark>>) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
- setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
- setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMark
- setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.FromSingleMark
- setMarkProvider(SingleMarkProvider) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnMarks
- setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
- setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
- setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RetrieveSingleMarkOnly
- setMarks(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
- setMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
-
The marks
- setMarks(MarkCollection) - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
- setMarks(Point2d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- setMarksColored(ColoredMarks) - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
- setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
- setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- setMarksExplicit(Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
- setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- setMarksExplicit(Point3d, Orientation) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- setMarksExplicit(Point3d, Orientation, Point2d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.ConicBase
- setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- setMarksExplicit(Point3d, Orientation, Point3d) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- setMarksOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
-
Deprecated.What's allowed or not when outputting configurations
- setMarksProposer(MarkCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
- setMarksProposer(MarkCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
- setMarksProposer(MarkCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
- setMask(Provider<Mask>) - Method in class org.anchoranalysis.image.bean.provider.MaskProviderUnary
- setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
- setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.FromMask
- setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
-
A mask that is provided to the stack.
- setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CheckMarkWithMask
- setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
- setMask(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.FromMaskBase
- setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
- setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.FromChannel
- setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
-
An optional mask which restricts the algorithm to only parts of the channel where the mask has an ON voxel
- setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.mask.AndObjectsWithMasks
- setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
- setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredMask
- setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.PairedWithMask
- setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.MaskAsSingleObject
- setMask(MaskProvider) - Method in class org.anchoranalysis.plugin.imagej.bean.object.provider.FillHoles
- setMaskElse(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfPredicateBase
-
Returned instead of
maskif the predicate is not satisfied - setMaskFilled(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
- setMaskFilled(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- setMaskIndex(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
- setMaskOutline(Provider<Mask>) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
- setMaskValue(int) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
-
What voxel value to read as "On" in the mask above.
- setMaskValue(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
- setMatch(String) - Method in class org.anchoranalysis.plugin.io.bean.input.filter.FilterCsvColumn
- setMatch(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.MatchedAppendCsv
- setMatch(RegEx) - Method in class org.anchoranalysis.feature.bean.list.SelectFromShared
- setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
- setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.feature.ObjectWithMaximumFeatureFromEachMatchedCollection
- setMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.Match
- setMatchString(String) - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
- setMax(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- setMax(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
- setMax(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
- setMax(double) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
- setMax(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.InvertedMax
- setMax(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
-
Boundary value indicating maximally-allowed range value
- setMax(int) - Method in interface org.anchoranalysis.core.progress.ProgressReporter
- setMax(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
- setMax(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
- setMax(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
- setMax(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
- setMax(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
- setMax(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.ClipHistogramMax
- setMax(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
- setMax(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
-
Calculates maximally-allowed range boundary
- setMax(UnitValueAreaOrVolume) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
-
Maximum-boundary for acceptable range
- setMaxCost(double) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
- setMaxCost(double) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
- setMaxDirectoryDepth(int) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
- setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
-
An optional maximum distance
- setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
- setMaxDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.onoutline.FindPointOnOutlineWalk
- setMaxDistanceBetweenMinima(UnitValueDistance) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
- setMaxDistanceCOG(UnitValueDistance) - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
-
The maximum distance allowed between center-of-gravities of objects
- setMaxDistanceDeltaContour(double) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
-
The maximum distance allowed between two seeds in terms of their values in the distance map
- setMaxDistanceDeltaContour(double) - Method in class org.anchoranalysis.plugin.ml.bean.cluster.MergeSpatialClusters
-
The maximum distance allowed between the 'distance from contour' values provided from the distanceMap for each point.
- setMaxDistanceProposer(ScalarProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
- setMaxDistanceZ(ScalarProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- setMaxIter(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.Repeat
- setMaxIter(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Repeat
- setMaxIter(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
- setMaxIter(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
- setMaxNumber(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.NumberIterations
- setMaxNumberItems(int) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Limit
- setMaxNumberProcessors(int) - Method in class org.anchoranalysis.experiment.bean.processor.DebugDependentProcessor
-
An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
- setMaxNumberProcessors(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
-
Theoretical maximum number of (CPU) processors to use in parallel.
- setMaxNumberProcessors(int) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
-
An upper limit on the number of the processors that can be simultaneously used in parallel, if they are available.
- setMaxNumberProcessors(int) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- setMaxNumItems(int) - Method in class org.anchoranalysis.plugin.io.bean.input.Limit
- setMaxNumItems(int) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.LimitWithDirectory
- setMaxSize(long) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
- setMaxSplitGroups(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- setMaxValue(long) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
- setMaxVar(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
- setMaxVolume(UnitValueAreaOrVolume) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
- setMaxX(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
-
Maximum X coordinate inclusive
- setMaxY(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
-
Maximum Y coordinate inclusive
- setMaxZ(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
-
Maximum Z coordinate inclusive
- setMean(double) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
-
Mean
- setMedian(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
-
If true, the median filter is included
- setMedianRadiusMeters(double) - Method in class org.anchoranalysis.plugin.imagej.bean.define.AddEdgeFilters
- setMerge(boolean) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
- setMergedPosTolerance(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.merge.MergeMarkEllipse
- setMergeMarkProposer(MarkMergeProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- setMessage(String) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
- setMethod(String) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
- setMethod(String) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
-
One of the following strings to identify ImageJ's thresholding algorithms (or an empty string for the default).
- setMin(double) - Method in class org.anchoranalysis.mpp.bean.bound.BoundMinMax
- setMin(double) - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
- setMin(double) - Method in class org.anchoranalysis.plugin.mpp.bean.check.RadiiMinRatio
- setMin(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareFromScalars
-
Boundary value indicating minimally-allowed range value
- setMin(int) - Method in interface org.anchoranalysis.core.progress.ProgressReporter
- setMin(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
- setMin(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
- setMin(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
- setMin(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
- setMin(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByMinMaxValue
- setMin(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.OutsideRange
- setMin(Feature<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
-
Calculates minimally-allowed range boundary
- setMin(UnitValueAreaOrVolume) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
-
Minimum-boundary for acceptable range
- setMinConfidence(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
-
The minimum confidence of an element for its object-mask to be included.
- setMinConfidence(double) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SegmentText
-
Proposed bounding boxes below this confidence interval are removed
- setMinDiff(double) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.MeanIntensityDifference
- setMinDifference(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
-
A minimum difference, below which 0.0 is returned
- setMinDifference(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
- setMinDiversity(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
- setMinimaImposition(MinimaImposition) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ImposeMinima
- setMinimumBoundingBoxVolume(int) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
-
Only objects whose bounding-box volume is greater or equal to this threshold are included.
- setMinIntensity(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.RejectIfIntensityLessThan
- setMinIntensity(int) - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
-
Intensity for thresholding
- setMinIntensityValue(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
- setMinMaxIgnoreBeforeIndex(int) - Method in class org.anchoranalysis.plot.index.LinePlot
- setMinMaxValues(int, int) - Method in class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
- setMinNumberObjects(int) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- setMinNumberPoints(int) - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
-
If a contour has less than this number of points, we don't split it, and return it as-is
- setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
-
Only includes squares that have at lesat this number of voxels
- setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
- setMinNumberVoxels(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
-
The minimum number of voxels that must exist in a connected-component to be included.
- setMinNumPoints(int) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
- setMinNumPoints(int) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
-
If an object has fewer points than before being fitted, we ignore
- setMinNumSlices(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- setMinNumZSlices(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.check.AtLeastZSlices
- setMinOverlap(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
- setMinRadius(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipseFitter
- setMinRadius(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
- setMinRadScaleEnd(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
- setMinRadScaleStart(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.split.MarkEllipseSimple
- setMinRatio(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- setMinRatioPointsInsideRegion(double) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- setMinSize(long) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.Mser
- setMinVal(double) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- setMinVolume(UnitValueAreaOrVolume) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.connected.ConnectedComponentsFromMask
- setMinVolume(UnitValueVolume) - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
- setMinVolumeConnectedComponent(UnitValueVolume) - Method in class org.anchoranalysis.plugin.fiji.bean.define.AddDistanceTransform
- setMinX(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
-
Minimum X coordinate inclusive
- setMinXYRes(double) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorMinXYRes
- setMinY(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
-
Minimum Y coordinate inclusive
- setMinZ(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.dimensions.InsideBoxOn
-
Minimum Z coordinate inclusive
- setMip(boolean) - Method in class org.anchoranalysis.image.feature.bean.object.single.NumberVoxels
- setMip(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
- setMip(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMIPBase
- setModelDirectory(Path) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
- setMultipleComparer(MultipleComparer) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
- setMultiplyBy(double) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
- setName(String) - Method in class org.anchoranalysis.bean.define.adder.FromXmlList
-
The name of the file in the current working directory WITHOUT THE .xml EXTENSION
- setName(String) - Method in class org.anchoranalysis.bean.NamedBean
-
The name associated with
item - setName(String) - Method in class org.anchoranalysis.bean.shared.path.RootPath
- setName(String) - Method in interface org.anchoranalysis.core.identifier.name.NameValue
-
Sets the associated namme
- setName(String) - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
- setName(String) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
- setName(String) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
- setName(String) - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
- setName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile
-
A name to describe the adjacent file
- setName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
-
The name of the appended entity
- setName(S, String) - Method in interface org.anchoranalysis.bean.permute.ApplyPermutations.NameSetter
- setNameLeft(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
- setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.io.bean.input.files.NamedFiles
- setNamer(FileNamer) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
Assigns each input a unique compact name.
- setNameRight(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- setNavigateHigherDirs(int) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
-
Search x number directories higher than file
- setNewNameOnFeature(Feature<? extends FeatureInput>, String, String) - Static method in class org.anchoranalysis.feature.bean.list.PrependName
- setNoBlack(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
- setNormalize(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Identity
- setNormalize(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.distance.BoundingBoxZOverlapRatio
- setNormalizeFeatures(boolean) - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderSVMClassifier
-
Normalize features
- setNumberChannels(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
- setNumberColors(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
- setNumberDilations(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
- setNumberFrames(int) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
- setNumberGPUProcessors(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
-
How many GPU processors to use when this is possible as a substitute for a CPU processor
- setNumberLoopPoints(int) - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
- setNumberPoints(int) - Method in class org.anchoranalysis.plot.index.LinePlot
- setNumberSubdirectories(int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
-
How many directories to include in the name.
- setNumBins(int) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
-
The number of bins in each histogram for a cell
- setNumCols(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
- setNumDecimalPlaces(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
- setNumLeadingZeros(int) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.FilePathCounter
- setNumLevelsGrouping(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- setNumMarks(int) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromMarkProposer
- setNumRep(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
- setNumRep(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingNumberMarks
- setNumRows(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Tile
- setObjectMatcher(ObjectMatcher) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Bridge
-
Used to match each intermediary-object to a final-object
- setObjects(List<NamedBean<ObjectCollectionProvider>>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- setObjects(Provider<ObjectCollection>) - Method in class org.anchoranalysis.image.bean.provider.ObjectCollectionProviderUnary
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureOnObjectsBase
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
-
The objects for whom a level is calculated
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.color.provider.GenerateToMatchObjects
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromObjects
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Always
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.match.Intersection
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredObjects
-
Objects to draw on a background
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.ObjectAggregationBase
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.ObjectAsPoints
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.IncludeRandomObjects
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.PointsFromObjects
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
- setObjects(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
- setObjects(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
-
Deprecated.What's allowed or not when outputting object-collections
- setObjects(OutputEnabled) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- setObjects1(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
-
First collection with items to be merged
- setObjects2(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeTwoCollectionsItemwise
-
Second collection with items to be merged
- setObjectsBlue(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
- setObjectsContainer(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
- setObjectsElse(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.ReferenceOrElse
- setObjectsGreater(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
- setObjectsGreen(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
- setObjectsGrouped(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.FilterByGroup
- setObjectsLesser(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
- setObjectsRed(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
- setObjectsRejected(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.ObjectCollectionProviderFilterBase
- setObjectsSave(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
-
Saves all objects that are inputs to the merge, outputs from the merge, or intermediate merges along the way
- setObjectsSeeds(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
- setObjectsSeeds(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
- setObjectsSource(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
- setObjectsSource(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
- setObjectsSplitBy(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
- setObjectsTarget(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignFromIntersectingObjects
- setOfConnectedComponentIDs() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- setOff(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
- setOff(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
- setOn(int, int, int) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
- setOn(Point3i) - Method in interface org.anchoranalysis.image.voxel.binary.BinaryOnOffSetter
- SetOperationFailedException - Exception in org.anchoranalysis.core.index
- SetOperationFailedException(String) - Constructor for exception org.anchoranalysis.core.index.SetOperationFailedException
- SetOperationFailedException(Throwable) - Constructor for exception org.anchoranalysis.core.index.SetOperationFailedException
- setOptimization(OptimizationScheme<VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.SegmentWithMarkedPointProcess
-
The optimization-scheme that determines which configurations are accepted/rejected from one iteration to the next.
- setOptionList(List<KernelProposerOption<T>>) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- setOptions(ReadOptions) - Method in class org.anchoranalysis.io.bioformats.bean.BioformatsReader
- setOptions(ReadOptions) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
- setOrientationProposer(OrientationProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
- setOrientationXYProposer(OrientationProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- setOutline(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
-
If true, an outline is drawn around the entries.
- setOutlineAtBoundary(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Outline
- setOutlineColor(RGBColorBean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
-
The color of the outline
- setOutlinePixelsRetriever(OutlinePixelsRetriever) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
- setOutlinePixelsRetrieverReverse(OutlinePixelsRetriever) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
- setOutlineProvider(MaskProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.bound.LineBoundCalculator
- setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
- setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
-
The width of the outline (only relevant if
outline==true - setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
-
The width of the outline.
- setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
-
The width of the outline
- setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
- setOutlineWidth(int) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- setOutPath(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
-
Constructs a path as an output, replacing $1, $2 etc.
- setOutPathPrefix(String) - Method in class org.anchoranalysis.io.output.bean.path.prefixer.PathPrefixerAvoidResolve
-
A directory in which to output the experiment-directory and files
- setOutput(String) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- setOutput(OutputManager) - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
-
The output-manager that specifies how/where/which elements occur duing outputting.
- setOutput(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
- setOutputCSV(boolean) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.Anonymize
-
Iff true, a mapping.csv file is created showing the mapping between the original-names and the anonymized versions
- setOutputDirectory(Optional<Path>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
-
A directory indicating where inputs can be located
- setOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
-
Deprecated.What's allowed or not - highest level outputs
- setOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- setOutputName(String) - Method in class org.anchoranalysis.experiment.bean.log.ToTextFileBase
-
The name to use (without extension) for the text-file log
- setOutputName(String) - Method in class org.anchoranalysis.io.output.namestyle.IndexableOutputNameStyle
- setOutputName(String) - Method in class org.anchoranalysis.io.output.namestyle.OutputNameStyle
-
An identifier used in rules to determine if an output is enabled or not.
- setOutputName(String) - Method in class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
- setOutputName(String) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.PeriodicSubdirectoryReporter
- setOutputName(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MinimalExecutionTimeStatsReporter
- setOutputName(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- setOutputNameStyle(IndexableOutputNameStyle) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.FromOutputName
- setOutputRGBOutline(StringSet) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- setOutputRGBOutlineFlattened(StringSet) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsAsCroppedImages
- setOutputsDisabled(StringSet) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
-
The names of the outputs that are disbled.
- setOutputsEnabled(StringSet) - Method in class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
-
The names of the outputs that are enabled.
- setOutputsEnabled(OutputEnabledRules) - Method in class org.anchoranalysis.io.output.bean.OutputManager
-
Which outputs are enabled or not enabled.
- setOutputShort(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
-
Iff true, outputs a short channel, otherwise byte channel
- setOutputStackProvider(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageAssignLabel
-
If it's set, a stack is generated that is outputted into subdirectory corresponding to the groupIdentifier.
- setOutputWriteSettings(OutputWriteSettings) - Method in class org.anchoranalysis.io.output.bean.OutputManager
-
General settings (default file extensions, colors etc.) for outtping files.
- setOutputWriteSettings(OutputWriteSettings) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- setOutside(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
-
Returned as a constant if a value lies otside the range
- setOutsideAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Erode
- setOutsideAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
- setOutsideAtThreshold(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.OutlineKernelBase
- setOverlapRatioThreshold(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- setOverlapThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ConditionallyMergeOverlappingObjects
-
The maximum size for merging.
- setPadding(Padding) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsBase
-
Padding placed on each side of the outputted image (if it's within the image)
- setPaddingXY(int) - Method in class org.anchoranalysis.image.bean.spatial.Padding
-
Padding placed on each side of the outputted image (if it's within the image) in XY directions
- setPaddingZ(int) - Method in class org.anchoranalysis.image.bean.spatial.Padding
-
Padding placed on each side of the outputted image (if it's within the image) in Z direction
- setPairAddCriteria(AddCriteriaPair) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- setPairCollection(RandomCollection<IdentifiablePair<Mark>>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- setPairTypeClass(Class<?>) - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- setParam(P) - Method in class org.anchoranalysis.bean.initializable.property.PropertyInitializer
-
Sets the current parameters used for propagation
- setParamMean(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
- setParamPrefix(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
- setParamPrefixAppendNumber(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFirstSecondOrder
-
If true the constant is appended to the param prefix (a dot and a number)
- setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
-
Parameters to optionally associated with
stackEnergy, and meaningless ifstackEnergyis not specified. - setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
- setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
- setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
- setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.ml.bean.classifier.FeatureListProviderLDAClassifier
- setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
- setParams(KeyValueParamsProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
- setParams(KeyValueParams) - Method in class org.anchoranalysis.feature.energy.EnergyStack
- setParams(HOGParameters) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
-
Parameters used for calculating HOG
- setParams(HOGParameters) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
-
Parameters used for calculating HOG
- setParamStdDev(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.GaussianSamplerFromParams
- setPath(String) - Method in class org.anchoranalysis.bean.shared.path.RootPath
-
A path on a filesystem to the directory, that defines the root
- setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
- setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.StaticFilePath
- setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.FilePathParser
- setPath(String) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- setPathAnnotation(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
- setPathDefaultMarks(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
- setPathLabel(DerivePath) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.ImageCSVLabeller
-
Path to a CSV label file (comma-separated, with header, no quotes)
- setPathParams(DerivePath) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
- setPaths(List<DerivePath>) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
-
All files need to be present
- setPaths(StringSet) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.FileSetFromStringSet
- setPenaltyValue(double) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.MaxOverlapRatio
- setPeriodTriggerBank(PeriodTriggerBank<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- setPermutation(AnchorBean<?>, Object) - Method in interface org.anchoranalysis.bean.permute.setter.PermutationSetter
- setPermutation(AnchorBean<?>, Object) - Method in class org.anchoranalysis.bean.permute.setter.PermutationSetterList
- setPermutation(AnchorBean<?>, Object) - Method in class org.anchoranalysis.bean.permute.setter.PermutationSetterSingle
- setPermutation(PermuteProperty<S>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
-
A permutation to apply.
- setPermutations(List<PermuteProperty<S>>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
-
A list of permutations to apply.
- setPermuteProperty(PermuteProperty<?>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Permute
- setPermuteProperty(PermuteProperty<Integer>) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDescribeIndex
- setPermuteProperty(PermutePropertySequenceInteger) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeatureSequenceInteger
- setPhysical(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
- setPlotBackgroundColor(RGBColorBean) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- setPlotGridlineColor(RGBColorBean) - Method in class org.anchoranalysis.plot.bean.colorscheme.PlotColorScheme
- setPoint(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- setPointConnectedComponentID(Point3i, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- setPointDirection(Point3i, int, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- setPoints(Point3d, Point3d) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- setPoints(Point3i, Point3i) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- setPointsFitter(String) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
-
Name of the
PointsFitterto use. - setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
- setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.plugin.points.bean.fitter.PointsFitterToMark
- setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ReflectInAxesWithinDistance
- setPointsFitter(PointsFitter) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
- setPointsFitter(PointsFitterToMark) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.collection.PointsFitterFromObjects
- setPointsFitter(PointsFitterToMark) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- setPointsFromOrientationProposer(PointsFromOrientationProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.MergeLists
- setPointsFromOrientationXYProposer(PointsFromOrientationProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
- setPointsProposer(PointsProposer) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
- setPos(Point3d) - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
- setPositionProposer(PositionProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.Position
- setPositionProposer(PositionProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.Repeat
- setPower(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.MeanRaisedToPower
- setPrefix(boolean) - Method in class org.anchoranalysis.bean.define.adder.FromXmlList
-
If true, a prefix is prepended to the name of each added bean.
- setPrefix(String) - Method in class org.anchoranalysis.bean.define.adder.DefineAdderWithPrefixBean
-
A prefix that is placed before the name of every bean created
- setPrefix(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
- setPrefix(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
- setPrependColor(RGBColorBean) - Method in class org.anchoranalysis.bean.shared.color.scheme.Prepend
- setPrependString(String) - Method in class org.anchoranalysis.feature.bean.list.ListSequence
- setPrependString(String) - Method in class org.anchoranalysis.feature.bean.list.PrependName
- setPrependString(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
- setPrependString(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
- setPreserveExtensionIfDuplicate(boolean) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RemoveExtensions
-
Keeps the extension if the file-name (without the extension) becomes duplicated with another
- setProbMapID(String) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.ProbabilityMap
- setProbNeg(double) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
- setProbPos(double) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.KernelPosNeg
- setProperty(String, Object) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- setPropertyPath(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyWithPath
-
Either a direct property of a bean e.g.
- setProposal(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
- setProposer(MarkFromCollectionProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.MarkFromCollectionProposerUnary
- setProposer(MarkProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.MarkProposerUnary
- setProvider(MarkCollectionProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromProvider
- setPxlPartMemo(MemoCollection) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputAllMemo
- setPxlPartMemo(VoxelizedMarkMemo) - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputSingleMemo
- setQuantile(double) - Method in class org.anchoranalysis.feature.bean.results.Quantile
-
The quantile.
- setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.QuantileStretch
- setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.Quantile
- setQuantile(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Quantile
- setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.shared.object.QuantileAcrossObjects
- setQuantile(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.stack.object.QuantileAcrossConnectedComponents
- setQuantileHigh(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
- setQuantileLow(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Range
- setQuantileLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
- setQuantileUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
- setRadiiProposer(RadiiProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.OrientationAndRadiiProposer
- setRadiiProposer(RadiiProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.RadiiProposerRepeat
- setRadius(double) - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- setRadius(double) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
- setRadius(int) - Method in class org.anchoranalysis.plugin.fiji.bean.mask.provider.AutoLocalThreshold
- setRadius(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBoundsWithoutRotation
- setRadiusBound(Bound) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
- setRadiusBound(Bound) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
- setRadiusInMeters(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
- setRadiusX(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- setRadiusY(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- setRadiusZ(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- setRate(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.annealing.Geometry
- setReceive(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.combine.CombineBase
- setRecurseSubfolders(boolean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
- setRecursive(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
Whether to apply the search recursively or not
- setRed(int) - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
- setRed(int) - Method in class org.anchoranalysis.core.color.RGBColor
- setRed(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
- setReduce(FeatureListElem<FeatureInputPairObjects>) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.FeatureListProviderAggregatePair
-
Method for reducing all pairs into a single value e.g.
- setReduce(ReduceElements<ObjectMask>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
-
The algorithm for reducing the number of object-masks.
- setReferencePoissonIntensity(double) - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
- setReferencesFeatureListCreator(StringSet) - Method in class org.anchoranalysis.feature.bean.list.ReferencedFeatures
-
Ensures any feature-lists mentioned here are evaluated, before this list is created.
- setReferencesFeatureListCreator(StringSet) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.permute.PermuteFeature
-
Makes sure a particular feature list creator is evaluated
- setRegex(String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.CopyFilesNamingOneRegEx
- setRegex(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
-
Regular expression to match against string
- setRegex(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
A regular-expression applied to the image file-path that matches three groups.
- setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.RegExMatcher
- setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.PathRegEx
-
Regular expression to use to match path with at least one group in it.
- setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.input.Exclude
- setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
-
The regular-expression to use for matching groups.
- setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.JoinRegExGroups
- setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.RemoveMatching
-
If a path matches a regular expression it is removed.
- setRegEx(RegEx) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
- setRegexAdjacent(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
This needs to be set if there is at least one adjacentChannel.
- setRegExDir(String) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
-
If non-empty a regular-expression is applied to directories
- setRegExFile(String) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
-
If non-empty a regular-expression is applied to files
- setRegExString(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.InsertRegExGroups
-
The regular-expression to use for matching groups, overloaded to handle legacy situations where a string is supplied.
- setRegion(MarkRegion) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
- setRegion(MarkRegion) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Intensity
- setRegionID(int) - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
- setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
- setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.stack.provider.ColoredMarks
- setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.FeatureMarkRegion
- setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
- setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.FeaturePairMemoSingleRegion
- setRegionID(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- setRegionID(int) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- setRegionMap(RegionMap) - Method in class org.anchoranalysis.mpp.feature.bean.energy.scheme.EnergySchemeCreatorByElement
- setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.mpp.bean.object.provider.FromMarks
- setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.AsObject
- setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
- setRegionMap(RegionMap) - Method in class org.anchoranalysis.plugin.points.bean.mark.provider.single.MarkProviderPointsFitterFromConvexHull
- setRejectIterationIfAllLow(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
- setRejectIterationIfDisconnected(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.morphological.Erode
- setRelation(RelationBean) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
- setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergePairs
-
Relation to threshold
- setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
- setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
- setRelation(RelationBean) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
- setRemoveExtensionInDescription(boolean) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
-
Whether to remove the file-extension from the filename.
- setRemoveTouchingBorderXY(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.assigner.FeatureCostAssigner
- setRepeat(int) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- setRepeats(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirth
-
Total number of births
- setReplaceMatchesWithSolids(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- setReplacement(String) - Method in class org.anchoranalysis.plugin.io.bean.copyfilesmode.naming.ApplyRegExSubstitution
- setReplacement(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Replace
-
What to replace in the path
- setReplacement(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.AdjacentFile
-
The replacement string used to determine the file
- setReplaceWithMidpoint(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeGreedyToIncreaseObjectFeature
- setReportFitterErrors(boolean) - Method in class org.anchoranalysis.plugin.points.bean.mark.proposer.single.FitPoints
- setRequireAllFilesMatch(boolean) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- setRequireArguments(RequireArguments) - Method in class org.anchoranalysis.experiment.bean.log.OnlyIf
-
The conditions that must be fulfilled
- setRequireArguments(RequireArguments) - Method in class org.anchoranalysis.mpp.segment.bean.optimization.feedback.FeedbackReceiverRequireArguments
- setRequireBBoxNeighbors(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
-
Requires for any potential merge that the bounding-boxes of the two objects must intersect or touch
- setRequireTouching(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithFeature
-
Requires the object-masks to touch.
- setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
-
If set, each channel is scaled to a specific size before the mean is calculated (useful for combining different sized images)
- setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGDescriptor
-
The input-image is rescaled to this width/height before calculating HOG descriptors
- setResizeTo(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGFeature
-
The input is rescaled to this width/height before calculating HOG descriptors
- setRestrictTo(MaskProvider) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.Invert
-
If set, the inversion only occurs on a particular region of the mask, as determined by this mask
- setResX(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
- setResY(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
- setResZ(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
- setRewardHigherSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
-
Treat the higher side as if it's the the fill cdf
- setRewardLowerSide(boolean) - Method in class org.anchoranalysis.plugin.operator.feature.bean.score.GaussianScore
- setRgb(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.FromChannelOrMask
-
If true, the output contains three channels (the input and two duplicates) instead of one
- setRoot1(double) - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
- setRoot2(double) - Method in class org.anchoranalysis.math.equation.QuadraticEquationSolver.QuadraticRoots
- setRootInStructure(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
If true the directory structure is ROOT/experiments/${ROOT_NAME}/${DATASET_NAME}_${DATASET_SUFFIX} If false, the directory structure is ROOT/experiments/${DATASET_NAME}_${DATASET_SUFFIX}
- setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.prefixer.Rooted
- setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.filepath.RootedFilePath
- setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
- setRootName(String) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Rooted
- setRootName(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
If non-empty then a rooted filesystem is used with this root
- setRootName(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
Root-name assuming multi-rooted strucutre
- setRootName(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentStructure
- setRootNameForStructure(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
If rootInStructure==true, the rootName is placed in the folder structure.
- setRotateOnlyIn2DPlane(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.orientation.LongestExtentWithin
- setRotationAngle(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.EllipseBounds
- setRotationAngle(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds2D
- setRotationBounds(RotationBounds3D) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.EllipsoidOrientationRadii
- setRotationX(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
- setRotationY(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
- setRotationZ(Bound) - Method in class org.anchoranalysis.mpp.bean.mark.bounds.RotationBounds3D
- setRotMatrix(DoubleMatrix2D) - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- setRow(int) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Cell
- setSampleEvery(int) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SampleWithDirectory
- setScalarProposer(ScalarProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.MaxWithConstant
- setScalarProposer(ScalarProposer) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Scale
- setScale(double) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
-
Standard-Deviation
- setScale(double) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
-
Whether to increase or reduce the size of the images
- setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.ScaleXY
- setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.ScaleXY
-
Determines how much to scale by
- setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.Scale
- setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.AtScale
- setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorInverted
- setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- setScaleCalculator(ScaleCalculator) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.collection.ScaleXY
- setScaleFactor(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.GradientBase
- setScaleLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
-
Sets the min by multiplying the quantileLower by this constant.
- setScaleLower(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
- setScaleRadii(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
- setScaleUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
-
Sets the max by multiplying the quantileUpper by this constant.
- setScaleUpper(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.convert.ScaleByParams
- setScore(VoxelScore) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreVoxels
- setScoreProvider(FeatureListProvider<FeatureInputStack>) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
- setScoreThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.reduce.NonMaximaSuppression
-
Bounding boxes with scores above this threshold are removed
- setSecond(boolean) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
-
Only relevant if time==true.
- setSecond(List<NamedBean<StringSet>>) - Method in class org.anchoranalysis.io.output.bean.rules.OutputEnableRulesSpecify
-
Output-names in the second-level (for all first level output-names)
- setSecond(StateTransformerBean<U, T>) - Method in class org.anchoranalysis.mpp.segment.transformer.Compose
-
Second transformation from
UtoT - setSecondary(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
-
If
proposalis true, this toggles between the primary and secondary proposal - setSecondary(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
- setSegment(BinarySegmentation) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationOne
- setSegment(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.SegmentChannel
-
Segmentation algorithm
- setSegment(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.ConnectedComponentsFromBinarySegmentation
- setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary
- setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannel
- setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentChannelByObject
- setSegment(SegmentChannelIntoObjects) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentWithSeeds
- setSegment(SegmentIntoMarks) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.segment.SegmentMarksFromImage
-
How to perform the segmentation.
- setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
-
The segmentation procedure.
- setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
-
The segmentation algorithm
- setSegment(SegmentStackIntoObjectsPooled<T>) - Method in class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
-
The segmentation algorithm that is applied as an input to non-maxima suppression.
- setSegmentStack(BinarySegmentation) - Method in class org.anchoranalysis.plugin.image.bean.object.segment.channel.SegmentOnMaximumIntensityAndExpandInZ
- setSelect(String) - Method in class org.anchoranalysis.plugin.image.feature.bean.list.pair.DeriveFromPair
-
Either "merged" or "first" or "second" indicating which feature to delegate from
- setSelectChannels(FromStacks) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
-
Selects which channels are included, optionally renaming.
- setSeperator(String) - Method in class org.anchoranalysis.feature.bean.list.ListSequence
- setSeperator(String) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- setSequence(SequenceInteger) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequence
-
Where the sequence starts
- setSequence(SequenceInteger) - Method in class org.anchoranalysis.feature.bean.list.ListSequence
-
First number range that is appended
- setSequence(OutputSequenceIndexed<T, S>) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
- setSequenceAdditional(SequenceInteger) - Method in class org.anchoranalysis.feature.bean.list.ListSequence
-
Another number range that is appended
- setShellRad(double) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipseFactory
- setShellRad(double) - Method in class org.anchoranalysis.mpp.bean.mark.factory.MarkEllipsoidFactory
- setShellRad(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- setShellRad(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- setShellRad(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
- setShellRad(double) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.CreateEllipse
- setShellRad(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
- setShift(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
- setShowAgg(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
- setShowBest(boolean) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.MemoryUsageReporter
- setShowDomainAxis(boolean) - Method in class org.anchoranalysis.plot.index.BarPlot
- setShowOngoingJobsLessThan(int) - Method in class org.anchoranalysis.experiment.bean.processor.ParallelProcessor
-
When the number of ongoing jobs is less than this threshold, they are shown in event logs.
- setShowVerticalAxisLines(boolean) - Method in class org.anchoranalysis.plot.PlotInstance
- setSigma(double) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
- setSigma(double) - Method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.GaussianBlur2D
- setSigmaInMeters(boolean) - Method in class org.anchoranalysis.plugin.image.bean.blur.BlurStrategy
- setSilentlyDeleteExisting(boolean) - Method in class org.anchoranalysis.io.output.bean.OutputManager
-
Whether to silently first delete any existing output at the intended path, or rather throw an error.
- setSilentlyDeleteExisting(boolean) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- setSimplePairCollectionID(String) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- setSize(double) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- setSize(int) - Method in class org.anchoranalysis.image.voxel.kernel.Kernel
- setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.plot.PlotHistogram
-
Size of the image produced showing a plot of the histogram
- setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
-
Size of all created thumbnails
- setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
- setSize(SizeXY) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- setSkipAtBorder(boolean) - Method in class org.anchoranalysis.plugin.imagej.bean.mask.provider.FillHoles
-
If true we do not fill any objects that touch the border
- setSkipFileName(boolean) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
-
Iff true the filename is not considered, only the subdirectories.
- setSkipFileName(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
- setSkipFirstTrim(int) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
- setSkipFirstTrim(int) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
- setSkipMissingChannels(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- setSkipNumberSubdirectories(int) - Method in class org.anchoranalysis.plugin.io.bean.descriptivename.LastDirectories
-
Initially skip this number of directories before including them in the description.
- setSlice(ChannelProvider) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.RepeatSlice
- setSliceEnd(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
- setSliceFirst(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
-
First slice.
- setSliceID(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
-
Index of slice to use, or -1 to use all slices
- setSliceIndex(int) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.slice.RepeatSlice
-
Which slice to use from
mask - setSliceLast(int) - Method in class org.anchoranalysis.plugin.imagej.bean.stack.provider.MontageSlices
-
Last slice.
- setSliceNum(Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
- setSlicesSeparately(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.resize.FitBoxToOnVoxels
- setSliceStart(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.slice.ExtractSliceRange
- setSmoothingFactor(double) - Method in class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
- setSource(String) - Method in class org.anchoranalysis.bean.shared.StringMapItem
- setSource(FeatureSource<T, S, U>) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.ExportFeatures
-
Source of feature-values to be exported
- setSourceFolderPath(FilePath) - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- setSplitDescriptiveNameRegex(String) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- setSplitProposer(MarkSplitProposer) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
- setSquareSize(int) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
- setStack(Provider<Stack>) - Method in class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
- setStack(StackProvider) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.ExportObjectsFromCSV
-
The stack that is the background for our objects
- setStack(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
- setStack(DisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
- setStack(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
-
Provides a stack.
- setStack(ProviderAsStack) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.segment.SegmentStack
-
The stack to segment
- setStackAsChannel(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.input.MultiInputManagerQuick
-
If true, a raster-stack is treated as a single-channel, even if multiple exist (and no additionalChannel is set)
- setStackBackground(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
- setStackEnergy(Provider<Stack>) - Method in class org.anchoranalysis.image.feature.bean.evaluator.FeatureEvaluator
-
Optionally specifies an energy-stack to be associated with every calculation input.
- setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
-
Optionally defines a energy-stack for feature calculation (if not set, the energy-stack is considered to be the input stacks)
- setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.labeller.BinaryClassifierImageLabeller
- setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.ExtractSlice
- setStackEnergy(StackProvider) - Method in class org.anchoranalysis.plugin.mpp.bean.define.DefineOutputterWithEnergy
- setStackID(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.predicate.IfStackExists
- setStackName(String) - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.One
-
If defined, processing only occurs the stack with this specific stack and index.
- setStackNameVisualOriginal(String) - Method in class org.anchoranalysis.annotation.io.bean.AnnotationBackground
- setStackProviderID(String) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.FromStack
-
Specifies the ID of an existing stack.
- setStackProviderID(String) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.convert.FromStackChannel
- setStackReader(StackReader) - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
- setStackReader(StackReader) - Method in class org.anchoranalysis.mpp.io.bean.input.MultiInputManager
- setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.annotation.bean.comparer.MaskComparer
- setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.AnnotationComparisonInputManager
- setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.GroupFiles
- setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
- setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannelsAppend
- setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
- setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.FlattenAsChannel
- setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ImposeResolution
- setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.MultiFileReader
- setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ReadVoxelExtentXml
- setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
- setStackReader(StackReader) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
The raster-reader for reading the main file
- setStackReaderAdjacent(StackReader) - Method in class org.anchoranalysis.plugin.quick.bean.input.NamedChannelsQuick
-
The raster-reader to use for opening any adjacent-channels
- setStackReaderAppend(StackReader) - Method in class org.anchoranalysis.plugin.quick.bean.input.QuickBase
-
The raster-reader for reading any appended files
- setStackReaderHigh(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- setStackReaderInput(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- setStackReaderLow(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- setStackReaderMiddle(StackReader) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- setStacksOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.output.LegacyOutputEnabled
-
Deprecated.What's allowed or not when outputting stacks
- setStacksOutputEnabled(OutputEnabled) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- setStart(int) - Method in class org.anchoranalysis.bean.permute.property.SequenceInteger
-
The index to begin iteration from
- setStartIndex(int) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- setStartingIntensity(int) - Method in class org.anchoranalysis.plugin.imagej.bean.object.segment.FloodFillEachIntensityLevel
-
The first intensity-value to consider as a valid object (e.g.
- setStateReporter(StateReporter<T, S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- setStrategy(BlurStrategy) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.intensity.Blur
- setStrongEdgeEnhancer(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.AnisotropicDiffusion
-
Enables the StrongEdgeEnhancer diffusion function
- setSubdirectory(String) - Method in class org.anchoranalysis.plugin.quick.bean.structure.ExperimentResultsExperimentStructure
-
If non-empty than an additional subdirectory is appended as a suffix ${DATASET_NAME}_${DATASET_SUFFIX}/${SUBDIRECTORY}/
- setSubDirectory(String) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.AppendKeyValueParams
- setSubtractConstant(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.gradient.IntensityGradientBase
- setSubtractFromMaskOnly(boolean) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
- setSubtractRadii(double) - Method in class org.anchoranalysis.plugin.points.bean.fitter.ConicFitterBase
- setSuffix(String) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertySequenceIntegerWithinString
- setSummarizer(Summarizer<S>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
- setSummarizer(Summarizer<S>) - Method in class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
- setSummarizerElse(Summarizer<T>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
-
Used for summary if
count(elements) <= countThreshold - setSummarizerGreaterThan(Summarizer<T>) - Method in class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
-
Used for summary if
count(elements) > countThreshold - setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.MorphologicalOperatorBase
- setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
- setSuppress3D(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.segment.binary.SegmentThresholdAboveMinBound
- setSuppressErrors(boolean) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.source.FromObjects
- setSuppressExceptions(boolean) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
- setSuppressExceptions(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- setSuppressExceptions(boolean) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- setSuppressOutlineZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.stack.provider.color.ColoredBase
-
if true, the outline is suppressed in the z-dimension i.e.
- setSuppressRes(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.radii.RadiiRatio
- setSuppressRootOut(boolean) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Rooted
-
if true, the root is not added to the outFilePath, and the path is instead localized against the location of the BeanXML.
- setSuppressSeries(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
-
If true, the series index is not included in the outputted file-names.
- setSuppressSubfolders(boolean) - Method in class org.anchoranalysis.mpp.segment.bean.define.DefineOutputter
- setSuppressZ(boolean) - Method in class org.anchoranalysis.mpp.feature.addcriteria.BoundingBoxIntersection
- setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransform3D
- setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.fiji.bean.channel.provider.distance.DistanceTransformForEachObject3D
- setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeWithOptionalDistanceConstraint
- setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.pair.overlap.CostOverlapWithinMidpointDistance
- setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
-
If true co-voariance is suprpessed in z-dimension
- setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.check.CenterOnMask
- setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.position.UniformRandom
- setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
- setSuppressZ(boolean) - Method in class org.anchoranalysis.plugin.points.bean.feature.object.conic.EllipsoidBase
-
Iff true, surpresses covariance in the z-direction.
- setSuppressZCovariance(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.mark.collection.FromObjects
- setSuppressZCovariance(boolean) - Method in class org.anchoranalysis.plugin.points.bean.fitter.LinearLeastSquaresEllipsoidFitter
- setTarget(String) - Method in class org.anchoranalysis.bean.shared.StringMapItem
- setTask(Task<MultiInput, S>) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- setTask(Task<T, S>) - Method in class org.anchoranalysis.experiment.bean.processor.JobProcessor
- setTask(Task<T, S>) - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- setTask(Task<T, S>) - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- setTask(Task<U, S>) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.ConvertNamedChannels
- setTask(SelectParam<Optional<Path>>) - Method in class org.anchoranalysis.launcher.executor.ExperimentExecutor
- setTaskName(Optional<String>) - Method in class org.anchoranalysis.experiment.ExperimentExecutionArguments
-
A name to describe the ongoing task
- setTaskProcessor(JobProcessor<T, S>) - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
-
What task is associated with the experiment, and how it is processed.
- setTemperature(double) - Method in class org.anchoranalysis.mpp.segment.optimization.step.OptimizationStep
- setTemplateMark(MarkFactory) - Method in class org.anchoranalysis.mpp.bean.mark.MarkWithIdentifierFactory
- setTermination(TerminationCondition) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
- setThreshold(double) - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- setThreshold(double) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
- setThreshold(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsThreshold
-
Only considers values greater or equal to the threshold
- setThreshold(double) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaFeatureRelationThreshold
- setThreshold(double) - Method in class org.anchoranalysis.plugin.mpp.bean.provider.single.RequireFeatureRelationThreshold
- setThreshold(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.provider.CutBelowThreshold
- setThreshold(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
- setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Count
- setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.RatioThreshold
- setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
- setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
- setThreshold(RelationToThreshold) - Method in class org.anchoranalysis.plugin.operator.feature.bean.conditional.IfCondition
- setThreshold(UnitValueDistance) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
- setThreshold(UnitValueDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.addcriteria.AddCriteriaDistanceTo
- setThreshold(UnitValueVolume) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
- setThresholder(Thresholder) - Method in class org.anchoranalysis.image.bean.segment.binary.BinarySegmentationThreshold
- setThresholder(Thresholder) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
-
The thresholder that will convert a channel into a binary-channel
- setThresholdHigh(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- setThresholdLow(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- setThrowExceptionForInsufficientPoints(boolean) - Method in class org.anchoranalysis.mpp.bean.points.CreateMarkFromPoints
- setThumbnail(ThumbnailFromObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
-
Generates a thumbnail representation of one or more objects combine, as form a single input
- setThumbnail(ThumbnailFromStack) - Method in class org.anchoranalysis.plugin.image.task.bean.feature.source.FromImage
-
Method to generate a thumbnail for images
- setTime(boolean) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierAuto
-
If true, the current time (HH.mm.ss) is included in the output
- setTimeIndex(int) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.ConvertNamedChannelsToStack
- setTimeIndex(Optional<Integer>) - Method in class org.anchoranalysis.plugin.io.multifile.FileDetails
- setTimeIndexGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- setTimes(int) - Method in class org.anchoranalysis.bean.shared.color.scheme.Repeat
- setTitle(String) - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
- setTitle(String) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
- setToleranceLog10(int) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
- setTransformer(StateTransformerBean<MarkCollection, T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartitionAndThen
- setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
- setTransformer(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
- setTransformerKernelToState(StateTransformerBean<U, T>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
- setTransformerMarks(StateTransformerBean<MarkCollection, VoxelizedMarksWithEnergy>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.AddDualTransformer
- setTransformerPrimary(StateTransformerBean<T, S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
- setTransformerSecondary(StateTransformerBean<T, S>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
- setTransformerStateToKernel(StateTransformerBean<T, U>) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
- setTransposed(boolean) - Method in class org.anchoranalysis.plugin.io.bean.task.CombineCSV
- setTrimTrailingDirectory(int) - Method in class org.anchoranalysis.plugin.quick.bean.file.path.derive.RemoveTrailingDirectory
- setTrimTrailingDirectory(int) - Method in class org.anchoranalysis.plugin.quick.bean.input.filepathappend.FilePathAppendBase
- setUniqueLabel(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
-
Label that uniquely identifies the ID (for machine purposes)
- setUnit(UnitConverter) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.BoundingBoxExtent
- setUnit(UnitConverter) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.FeatureSingleMemoRegion
- setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
- setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
- setUnitType(String) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
- setUnitType(String) - Method in class org.anchoranalysis.image.feature.bean.physical.convert.FeatureConvertUnits
- setUnitType(String) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
- setUnitTypeFrom(String) - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
- setUnitTypeTo(String) - Method in class org.anchoranalysis.plugin.operator.feature.physical.ConvertUnits
- setUnitValueDistance(UnitValueDistance) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.FromUnitValueDistance
- setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.ConvertTo
-
Always called before any batch of calls to
ConvertTo.convertSliceOfSingleChannel(java.nio.ByteBuffer, int). - setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
- setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
- setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
- setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
- setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
- setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
- setupBefore(Dimensions, int) - Method in class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
- SetUpdatable - Class in org.anchoranalysis.mpp.bean.points.updatable
- SetUpdatable() - Constructor for class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- setupParams(KeyValueParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.FromParamsBase
- setupParams(KeyValueParams) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.GaussianFromParams
- setUseLastSeriesIndexOnly(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.channel.NamedChannels
- setUseLastSeriesIndexOnly(boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
- setUseMax(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatio
- setUseMax(boolean) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapRatioMask
- setUseMIP(boolean) - Method in class org.anchoranalysis.annotation.io.bean.comparer.MultipleComparer
- setUseMIP(boolean) - Method in class org.anchoranalysis.plugin.annotation.bean.comparison.CompareAnnotations
- setUserFriendlyLabel(String) - Method in class org.anchoranalysis.plugin.annotation.bean.label.AnnotationLabel
-
Descriptive user-friendly label displayed via GUI
- setUseZ(boolean) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.filter.RemoveTouchingBorder
- setUseZ(boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
- setValue(double) - Method in class org.anchoranalysis.feature.bean.operator.Constant
- setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistancePhysical
- setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.distance.DistanceVoxels
- setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
- setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
- setValue(double) - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
- setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.assign.AssignValue
- setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
- setValue(double) - Method in class org.anchoranalysis.plugin.image.bean.scale.ScaleCalculatorConstant
- setValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.IdentityImposeValueRelationToHistogram
- setValue(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.NormalizeByConstant
- setValue(double) - Method in class org.anchoranalysis.plugin.io.bean.stack.reader.RejectIfConditionXYResolution
- setValue(double) - Method in class org.anchoranalysis.plugin.mpp.bean.proposer.scalar.Constant
- setValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
- setValue(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.CreateNew
- setValue(int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.EmptyHistogramConstant
- setValue(int) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.CountEqual
- setValue(String) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
- setValue(String) - Method in class org.anchoranalysis.plugin.image.bean.params.KeyValueCondition
- setValue(String) - Method in class org.anchoranalysis.plugin.io.bean.path.derive.Constant
- setValue(T) - Method in class org.anchoranalysis.bean.NamedBean
- setValue(T) - Method in interface org.anchoranalysis.core.identifier.name.NameValue
-
Sets the associated value
- setValue(V) - Method in class org.anchoranalysis.core.identifier.name.SimpleNameValue
- setValueByDimension(int, double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- setValueByDimension(int, float) - Method in class org.anchoranalysis.spatial.point.Tuple3f
- setValueIfEmpty(double) - Method in class org.anchoranalysis.image.feature.histogram.FeatureHistogramStatistic
-
The value to return iff
exceptionifEmptyis false - setValueIfTooFewVoxels(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.ImageMomentsBase
-
A value to return if there are too few voxels (less than
MIN_NUM_VOXELSto calculate moments - setValueNoObject(int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.score.ScoreObjects
- setValueNoObjects(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
- setValues(StringSet) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyDoubleSet
- setValues(StringSet) - Method in class org.anchoranalysis.bean.permute.property.PermutePropertyStringSet
-
The values of the string-set
- setVaryColors(boolean) - Method in class org.anchoranalysis.plugin.image.task.bean.segment.SegmentInstanceWithModel
-
If true the colors change for different objects in the image (using a default color set).
- setVersion(String) - Method in class org.anchoranalysis.experiment.bean.identifier.ExperimentIdentifierConstant
- setVerticalAlign(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
- setVisitScheduler(VisitScheduler) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
- setWeight(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionSingle
- setWeightBackground(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
- setWeightForeground(double) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.OtsuWeighted
- setWeightItem1Greater(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
- setWeightItem2Greater(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.Range
- setWeightNegative(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
- setWeightPositive(double) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.proposer.KernelProposerOptionDual
- setWeightWidthDescription(int) - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
- setWhenDetailed(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
-
Logger to use when detailed-logging is on
- setWhenEqual(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
- setWhenNot(LoggingDestination) - Method in class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
-
Logger to use when detailed-logging is off
- setWhenNotEqual(ObjectCollectionProvider) - Method in class org.anchoranalysis.plugin.image.bean.object.provider.IfParamEqual
- setWhenOneOrThreeChannels(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
-
Writer employed if a stack is a one or three-channeled image, that is not 3D, and not RGB.
- setWhenRGB(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
-
Writer employed if a stack is a three-channeled RGB image and is not 3D.
- setWidth(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.Difference
-
Width (what the difference is divided by)
- setWidth(int) - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
- setWidthFactor(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.score.DifferenceCalculateLevelStandardDeviation
- setWindowSize(int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
- setWindowSize(SizeXY) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
-
The window-size as per OpenCV implementation.
- setWithin(double) - Method in class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
-
Returned as a constant if a value lies within the range
- setWithinValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
-
Constant to return if value lies within the range
- setWithinValue(double) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
-
Constant to return if value lies within the range
- setWriter(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchChannels
-
Default writer, if a more specific writer is not specified for a condition.
- setWriter(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
- setWriterAlways2D(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
-
Writer to use if it is guaranteed that the image will always be 2D.
- setWriterElse(StackWriter) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.BranchStack
-
Otherwise the writer to use.
- setWriters(List<NamedBean<?>>) - Method in class org.anchoranalysis.io.output.bean.OutputWriteSettings
-
Specifies a writer bean instance for a particular type of writer (identified by the writer bean class)
- setX(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
- setX(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- setX(int) - Method in class org.anchoranalysis.spatial.point.Point2i
- setX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- setX(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- setX(String) - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
- setXY(String, String) - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
- setY(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
- setY(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- setY(int) - Method in class org.anchoranalysis.spatial.point.Point2i
- setY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- setY(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- setY(String) - Method in class org.anchoranalysis.plot.index.PlotAxisLabels
- setYAxisLowerMargin(double) - Method in class org.anchoranalysis.plot.index.LinePlot
- setYAxisMargins(double) - Method in class org.anchoranalysis.plot.index.LinePlot
- setYAxisUpperMargin(double) - Method in class org.anchoranalysis.plot.index.LinePlot
- setYValGetter(LinePlot.YValGetter<T>) - Method in class org.anchoranalysis.plot.index.LinePlot
- setZ(double) - Method in class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
- setZ(double) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- setZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- setZ(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- setZAlign(String) - Method in class org.anchoranalysis.image.bean.spatial.arrange.Overlay
- setZOnly(boolean) - Method in class org.anchoranalysis.plugin.image.bean.mask.provider.morphological.Dilate
- setZSliceGroupID(int) - Method in class org.anchoranalysis.plugin.io.bean.groupfiles.parser.RegExpFilePathParser
- setZSliceNum(int) - Method in class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
- SgmnMPPState - Class in org.anchoranalysis.plugin.mpp.segment
- SgmnMPPState(KernelProposer<VoxelizedMarksWithEnergy>, Define) - Constructor for class org.anchoranalysis.plugin.mpp.segment.SgmnMPPState
- shallowCopy() - Method in class org.anchoranalysis.core.color.ColorList
- shallowCopy() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
Creates a new graph with identical elements and structure, reusing the existing vertice and edge data objects.
- shallowCopy() - Method in class org.anchoranalysis.feature.name.FeatureNameList
- shallowCopy() - Method in class org.anchoranalysis.mpp.feature.addcriteria.RandomCollectionWithAddCriteria
- shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
-
Make a shallow copy
- shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
-
Creates a shallow-copy of the marks
- shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedAll
- shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- shallowCopy() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
- shallowCopy() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- shallowCopy() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- shallowCopy() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- shallowDuplicate() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
-
Creates a new feature-list which contains identical elements
- ShapeRegularityCenterSlice - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
- ShapeRegularityCenterSlice() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityCenterSlice
- ShapeRegularityMIP - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.shape
- ShapeRegularityMIP() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.shape.ShapeRegularityMIP
- SharedFeatureMulti - Class in org.anchoranalysis.feature.shared
-
A group of features (of possibly heterogeneous type) made available to other features to reference
- SharedFeatureMulti() - Constructor for class org.anchoranalysis.feature.shared.SharedFeatureMulti
- SharedFeatureSet<T extends FeatureInput> - Class in org.anchoranalysis.feature.shared
- SharedFeatureSet(NameValueSet<Feature<T>>) - Constructor for class org.anchoranalysis.feature.shared.SharedFeatureSet
- SharedFeaturesInitParams - Class in org.anchoranalysis.feature.shared
- SharedObjects - Class in org.anchoranalysis.core.identifier.provider.store
-
Objects shared between different components.
- SharedObjects(CommonContext) - Constructor for class org.anchoranalysis.core.identifier.provider.store.SharedObjects
- sharedObjectsRequired() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
- SharedStateExportFeatures<S> - Class in org.anchoranalysis.plugin.image.task.feature
-
Shared-state for an export-features class
- SharedStateExportFeatures(ResultsWriterMetadata, Supplier<S>, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
-
Creates the shared state.
- SharedStateFilteredImageOutput<T> - Class in org.anchoranalysis.plugin.image.task.labeller
- SharedStateFilteredImageOutput(Outputter, ImageLabeller<T>) - Constructor for class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
- SharedStateSegmentInstance<T> - Class in org.anchoranalysis.plugin.image.task.segment
-
Shared-state for instance segmentation
- SharedStateSegmentInstance(ConcurrentModelPool<T>, FeatureTableCalculator<FeatureInputSingleObject>, LabelHeaders, InputOutputContext) - Constructor for class org.anchoranalysis.plugin.image.task.segment.SharedStateSegmentInstance
- SharedStateSelectedSlice - Class in org.anchoranalysis.plugin.image.task.slice
- SharedStateSelectedSlice(Outputter) - Constructor for class org.anchoranalysis.plugin.image.task.slice.SharedStateSelectedSlice
- Shell - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.morphological
- Shell() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.morphological.Shell
- shift() - Method in class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
-
Increments the slice number by one
- shiftBackBy(VoxelsAssigner, ReadableTuple3i) - Static method in class org.anchoranalysis.image.voxel.assigner.VoxelsAssignerFactory
-
Shifts all coordinates BACKWARDS before passing to another
VoxelsAssigner. - shiftBackBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Shifts the object-mask by moving its bounding-box backwards (i.e.
- shiftBackBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
Shifts the bounding-box backwards.
- shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
-
Shifts the bounding-box of each object by adding to it i.e.
- shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Shifts the object-mask by moving its bounding-box forwards (i.e.
- shiftBy(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
Shifts the bounding-box forwards.
- shiftBy(T, ReadableTuple3i) - Method in interface org.anchoranalysis.image.core.object.scale.AccessObjectMask
-
Positionally-shifts an element by a given quantity in the positive direction.
- shiftTo(Point3i) - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
Assigns a new corner-location to the bounding-box.
- shiftToOrigin() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
Creates a new object-mask with identical voxels but with the bounding-box beginning at the origin (0,0,0)
- shiftToOrigin() - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
Moves the bounding-box to the origin (0,0,0) but preserves the extent
- shiftToZ(int) - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
Assigns a new z-slice corner-location to the bounding-box
- SHORT_OPTION_DEBUG - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
- SHORT_OPTION_HELP - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
- SHORT_OPTION_INPUT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
- SHORT_OPTION_LOG_ERROR - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
- SHORT_OPTION_OUTPUT - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
- SHORT_OPTION_OUTPUT_DISABLE_ADDITIONAL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
- SHORT_OPTION_OUTPUT_ENABLE_ADDITIONAL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
- SHORT_OPTION_OUTPUT_ENABLE_ALL - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
- SHORT_OPTION_SHOW_EXPERIMENT_ARGUMENTS - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
- SHORT_OPTION_TASK - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
- SHORT_OPTION_VERSION - Static variable in class org.anchoranalysis.launcher.options.CommandLineOptions
- shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.ArithmeticWithConstantConditionallyWriteBase
-
Whether to overwrite the current voxel-value with the constant?
- shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MaxWithConstant
- shouldOverwriteVoxelWithConstant(int, int) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.MinWithConstant
- shuffle() - Method in class org.anchoranalysis.core.color.ColorList
- Shuffle - Class in org.anchoranalysis.bean.shared.color.scheme
-
Randomizes the order of the colors from existing scheme.
- Shuffle<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Randomly shuffles the order of an input-manager
- Shuffle() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Shuffle
- Shuffle() - Constructor for class org.anchoranalysis.plugin.io.bean.input.Shuffle
- Shuffle(ColorScheme) - Constructor for class org.anchoranalysis.bean.shared.color.scheme.Shuffle
- SignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype
- SignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype
- SignedVoxelType(int, String, long, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.SignedVoxelType
- SimpleAnnotationDeleter - Class in org.anchoranalysis.annotation.io
-
Deletes any annotation that is only the file represented at the path
- SimpleAnnotationDeleter() - Constructor for class org.anchoranalysis.annotation.io.SimpleAnnotationDeleter
- SimpleCopy - Class in org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod
- SimpleCopy() - Constructor for class org.anchoranalysis.plugin.io.bean.copyfilesmode.copymethod.SimpleCopy
- SimpleManifestDeserializer - Class in org.anchoranalysis.io.manifest.deserializer
- SimpleManifestDeserializer() - Constructor for class org.anchoranalysis.io.manifest.deserializer.SimpleManifestDeserializer
- SimpleName - Class in org.anchoranalysis.feature.io.name
-
A name with only one part, and is always unique.
- SimpleName(String) - Constructor for class org.anchoranalysis.feature.io.name.SimpleName
- SimpleNameValue<V> - Class in org.anchoranalysis.core.identifier.name
-
A simple container expressing a name-value pair
- SimpleNameValue(String, V) - Constructor for class org.anchoranalysis.core.identifier.name.SimpleNameValue
- SimpleOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
- SimpleOutputNameStyle(String) - Constructor for class org.anchoranalysis.io.output.namestyle.SimpleOutputNameStyle
- SimpleOverlayWriter - Class in org.anchoranalysis.mpp.io.marks.generator
-
Converts a configuration to a set of object-masks, using a simple
DrawObjectfor all objects. - SimpleOverlayWriter(DrawObject) - Constructor for class org.anchoranalysis.mpp.io.marks.generator.SimpleOverlayWriter
- SimplePropertyDefiner<P> - Class in org.anchoranalysis.bean.initializable.property
- SimplePropertyDefiner(Class<?>) - Constructor for class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
- SimulatedAnnealing<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
-
Finds an optima using a simulated-annealing approach
- SimulatedAnnealing() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.SimulatedAnnealing
- Single - Class in org.anchoranalysis.image.bean.spatial.arrange
- Single - Class in org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition
- Single() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Single
- Single() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
- SingleChannel - Class in org.anchoranalysis.plugin.image.feature.bean.score
-
A score that is calculated on a single channel only
- SingleChannel - Class in org.anchoranalysis.plugin.io.bean.channel.map
-
For an image with a single channel
- SingleChannel() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.score.SingleChannel
- SingleChannel() - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
- SingleChannel(String) - Constructor for class org.anchoranalysis.plugin.io.bean.channel.map.SingleChannel
- SingleColor - Class in org.anchoranalysis.core.color
-
An index that always uses the same single color
- SingleColor(Color) - Constructor for class org.anchoranalysis.core.color.SingleColor
- SingleColor(RGBColor) - Constructor for class org.anchoranalysis.core.color.SingleColor
- SingleContainer<T> - Class in org.anchoranalysis.core.index.bounded
- SingleContainer(boolean) - Constructor for class org.anchoranalysis.core.index.bounded.SingleContainer
- SingleContainer(T, int, boolean) - Constructor for class org.anchoranalysis.core.index.bounded.SingleContainer
- SingleFileTypeGenerator<T,S> - Class in org.anchoranalysis.io.generator
-
A
Generatorthat eventually writes only a single file to the filesystem. - SingleFileTypeGenerator() - Constructor for class org.anchoranalysis.io.generator.SingleFileTypeGenerator
- SingleFileTypeGeneratorBridge<S,T,V> - Class in org.anchoranalysis.io.generator
-
Allows us to call an
SingleFileTypeGenerator<V,S>as if it was anSingleFileTypeGenerator<T,S>using an function to connect the two. - SingleFileTypeGeneratorBridge(SingleFileTypeGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
- SingleLevelAnd - Class in org.anchoranalysis.io.output.enabled.single
-
Outputs are enabled if they are contained in both of two
SingleLevelOutputEnabled. - SingleLevelAnd(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelAnd
-
Creates using two
SingleLevelOutputEnableds. - SingleLevelBinary - Class in org.anchoranalysis.io.output.enabled.single
-
Base class for a
SingleLevelOutputEnabledthat combines two existing such classes. - SingleLevelBinary(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelBinary
- SingleLevelInSet - Class in org.anchoranalysis.io.output.enabled.single
-
Outputs are enabled if they are contained in a set.
- SingleLevelInSet(Set<String>) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelInSet
- SingleLevelNot - Class in org.anchoranalysis.io.output.enabled.single
-
The complement of an existing
SingleLevelOutputEnabledwhere disabled outputs are enabled, and vice-versa. - SingleLevelNot(SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelNot
- SingleLevelOr - Class in org.anchoranalysis.io.output.enabled.single
-
Outputs are enabled if they are contained in either of two
SingleLevelOutputEnabled. - SingleLevelOr(SingleLevelOutputEnabled, SingleLevelOutputEnabled) - Constructor for class org.anchoranalysis.io.output.enabled.single.SingleLevelOr
-
Creates using two
SingleLevelOutputEnableds. - SingleLevelOutputEnabled - Interface in org.anchoranalysis.io.output.enabled.single
- SingleMarkProvider - Class in org.anchoranalysis.mpp.bean.provider
-
Provides (maybe) a single mark
- SingleMarkProvider() - Constructor for class org.anchoranalysis.mpp.bean.provider.SingleMarkProvider
- SingleObjectFromChannelFactory - Class in org.anchoranalysis.image.core.object.factory
- SingleObjectFromPointsFactory - Class in org.anchoranalysis.image.core.object.factory
- SinglePathStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
- SinglePathStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.SinglePathStrategy
- singleProcessor(int) - Static method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
-
Creates a plan for a single-CPU processor
- SingleRowPerInput<T extends InputFromManager,S extends FeatureInput> - Class in org.anchoranalysis.plugin.image.task.bean.feature.source
-
Base class for exporting features, where features are calculated per-image using a
NamedFeatureStore. - SingleRowPerInput(String) - Constructor for class org.anchoranalysis.plugin.image.task.bean.feature.source.SingleRowPerInput
- SingleTableCalculator - Class in org.anchoranalysis.image.feature.session
- SingleTableCalculator(NamedFeatureStore<FeatureInputSingleObject>) - Constructor for class org.anchoranalysis.image.feature.session.SingleTableCalculator
- size() - Method in class org.anchoranalysis.core.color.ColorList
- size() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
- size() - Method in class org.anchoranalysis.feature.bean.list.FeatureList
- size() - Method in class org.anchoranalysis.feature.list.NamedFeatureStore
- size() - Method in class org.anchoranalysis.feature.name.FeatureNameList
- size() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
- size() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
- size() - Method in class org.anchoranalysis.image.core.object.scale.ScaledElements
-
Number of scaled-elements.
- size() - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- size() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
- size() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
- size() - Method in class org.anchoranalysis.image.core.stack.NamedStacks
-
Number of stacks
- size() - Method in class org.anchoranalysis.image.core.stack.TimeSequence
- size() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
- size() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
- size() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
- size() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
- size() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapperList
- size() - Method in class org.anchoranalysis.math.histogram.Histogram
-
The number of items in the histogram
(maxBin - minBin + 1) - size() - Method in class org.anchoranalysis.mpp.bean.bound.BoundUnitless
- size() - Method in class org.anchoranalysis.mpp.bean.points.updatable.SetUpdatable
- size() - Method in class org.anchoranalysis.mpp.bean.points.updatable.UpdatablePointsContainer
- size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithTotalEnergy
- size() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- size() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedInd
- size() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- size() - Method in class org.anchoranalysis.mpp.feature.mark.MemoCollection
- size() - Method in class org.anchoranalysis.mpp.feature.mark.MemoList
- size() - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- size() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- size() - Method in interface org.anchoranalysis.mpp.mark.voxelized.memo.MemoForIndex
- size() - Method in class org.anchoranalysis.mpp.probmap.ProbWeights
- size() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
- size() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
- size() - Method in class org.anchoranalysis.mpp.voxel.partition.IndexByChannel
- size() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- size() - Method in class org.anchoranalysis.overlay.collection.OverlayCollection
- size() - Method in class org.anchoranalysis.plugin.image.feature.object.ListWithThumbnails
- size() - Method in class org.anchoranalysis.plugin.io.multifile.ParsedFilePathBag
- size() - Method in class org.anchoranalysis.spatial.box.BoundedList
-
The number of elements
- size() - Method in class org.anchoranalysis.spatial.rtree.RTree
- Size - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
- Size() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.Size
- sizeBytes - Variable in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
- sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
- sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberChannels
- sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
- sizeC(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
- sizeCurrentLoad() - Method in class org.anchoranalysis.core.cache.LRUCache
-
Number of items currently in the cache
- sizeCurrentLoad() - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
-
Number of items currently in the cache
- sizeDescriptor(Extent) - Method in class org.anchoranalysis.plugin.opencv.bean.feature.HOGParameters
-
Calculates the size of the descriptor will be for a given image, assuming the window is equal to the image-size
- SizeExtents - Class in org.anchoranalysis.plugin.io.multifile
-
Remembers the different sizes among the files
- SizeExtents(ParsedFilePathBag) - Constructor for class org.anchoranalysis.plugin.io.multifile.SizeExtents
- sizeFeatures() - Method in class org.anchoranalysis.feature.session.calculator.cached.FeatureCalculatorCachedMulti
- sizeFeatures() - Method in interface org.anchoranalysis.feature.session.calculator.FeatureCalculatorMulti
-
The number of features that is calculated on each call to calc(), and therefore the size of the ResultsVector returned
- sizeFeatures() - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiChangeInput
- sizeFeatures() - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiFromSingle
- sizeFeatures() - Method in class org.anchoranalysis.feature.session.calculator.FeatureCalculatorMultiReuse
- sizeFeatures() - Method in class org.anchoranalysis.feature.session.SequentialSession
- sizeFeatures() - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
- sizeFeatures() - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
- sizeFirst() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
-
The number of elements in the first list.
- sizeSecond() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
-
The number of elements in the second list.
- sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
- sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceNumberFrames
- sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
- sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
- sizeT(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
- sizeXY - Variable in class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
- SizeXY - Class in org.anchoranalysis.image.bean.spatial
- SizeXY() - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY
- SizeXY(int, int) - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY
- SizeXY(Extent) - Constructor for class org.anchoranalysis.image.bean.spatial.SizeXY
-
Constructor
- sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.Default
- sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ForceTimeSeriesToStack
- sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptions
- sizeZ(IFormatReader) - Method in class org.anchoranalysis.io.bioformats.bean.options.ReadOptionsDelegate
- skewness(Histogram) - Static method in class org.anchoranalysis.math.histogram.HistogramStatistics
- Skewness - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- Skewness() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Skewness
- SkipInit - Annotation Type in org.anchoranalysis.bean.annotation
-
Indicates that this particular bean-field should be ignored during (recursive) initialisation
- slice(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- slice(int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
- slice(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
-
Creates a new
Voxelswith only particular slice - slice(int) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromByte
- slice(int) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromFloat
- slice(int) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromInt
- slice(int) - Method in class org.anchoranalysis.image.voxel.factory.sliceindex.FromShort
- slice(int) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
- slice(int) - Method in class org.anchoranalysis.image.voxel.Voxels
- slice(int) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- SliceAt - Class in org.anchoranalysis.plugin.image.bean.object.provider.slice
- SliceAt() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.slice.SliceAt
- sliceBuffer(int) - Method in class org.anchoranalysis.image.core.mask.Mask
- sliceBuffer(int) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- sliceBuffer(int) - Method in interface org.anchoranalysis.image.voxel.factory.sliceindex.SliceBufferIndex
- sliceBuffer(int) - Method in class org.anchoranalysis.image.voxel.Voxels
- sliceBufferGlobal(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
A slice buffer with global coordinates
- sliceBufferGlobal(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
A slice buffer with global coordinates
- SliceBufferIndex<T> - Interface in org.anchoranalysis.image.voxel.factory.sliceindex
-
Provides voxel-buffers for each z-slice.
- sliceBufferLocal(int) - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- sliceBufferLocal(int) - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
A slice buffer with local coordinates i.e.
- sliceBufferLocal(int) - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
A slice buffer with local coordinates i.e.
- slices() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- slices() - Method in class org.anchoranalysis.image.voxel.Voxels
- sliceStatisticsForRegion(VoxelizedMark, int) - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- SliceThresholder - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
- SliceThresholder(BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder
- SliceThresholderMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
- SliceThresholderMask(boolean, ObjectMask, BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderMask
- SliceThresholderWithoutMask - Class in org.anchoranalysis.plugin.image.segment.thresholder.slice
- SliceThresholderWithoutMask(BinaryValuesByte) - Constructor for class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholderWithoutMask
- SlidingBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer
-
Contains the buffer for the current slice, the current slice minus 1, and the current slice plus 1
- SlidingBuffer(Voxels<T>) - Constructor for class org.anchoranalysis.image.voxel.buffer.SlidingBuffer
- Sobel - Class in org.anchoranalysis.plugin.image.bean.channel.provider.gradient
-
3x3 Sobel Filter
- Sobel() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.gradient.Sobel
- solveQuadraticEquation(double, double, double) - Static method in class org.anchoranalysis.math.equation.QuadraticEquationSolver
-
Solves a quadratic equation in form x^2 + b^x + c = 0
- sort(Comparator<Feature<T>>) - Method in class org.anchoranalysis.feature.bean.list.FeatureList
-
Creates a new feature-list sorted in a particular order.
- SortAlphabetically<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.input
-
Sorts the input-items in alphabetical order of their input-name.
- SortAlphabetically - Class in org.anchoranalysis.plugin.io.bean.provider.file
- SortAlphabetically() - Constructor for class org.anchoranalysis.plugin.io.bean.input.SortAlphabetically
- SortAlphabetically() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.SortAlphabetically
- SortAlphabeticallyWithDirectory - Class in org.anchoranalysis.plugin.io.bean.provider.file
- SortAlphabeticallyWithDirectory() - Constructor for class org.anchoranalysis.plugin.io.bean.provider.file.SortAlphabeticallyWithDirectory
- SortByFeature - Class in org.anchoranalysis.plugin.image.bean.object.provider.feature
-
Creates a new object-collection with objects sorted by a derived feature-value (in ascending order)
- SortByFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.feature.SortByFeature
- SortedSetChannel - Class in org.anchoranalysis.plugin.io.multifile
- SortedSetChannel() - Constructor for class org.anchoranalysis.plugin.io.multifile.SortedSetChannel
- SortedSetSlice - Class in org.anchoranalysis.plugin.io.multifile
- SortedSetSlice(String, int) - Constructor for class org.anchoranalysis.plugin.io.multifile.SortedSetSlice
- sourceVal - Variable in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
- spatiallySeparate() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollectionRTree
-
Splits the collection of objects into spatially separate clusters.
- SpatiallySeparate<T> - Class in org.anchoranalysis.spatial.rtree
- SpatiallySeparate(Function<T, BoundingBox>) - Constructor for class org.anchoranalysis.spatial.rtree.SpatiallySeparate
- SpatialUnits - Class in org.anchoranalysis.image.core.dimensions
-
Units to describe spatial quantities.
- SpatialUnits.UnitSuffix - Enum in org.anchoranalysis.image.core.dimensions
-
Suffix that describes a particular quantity of units (micron, nano, square microns etc.)
- Specific - Class in org.anchoranalysis.plugin.mpp.bean.region
- Specific() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.Specific
- SpecificAndRename - Class in org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels
-
Selects a specific set of channels from stacks, each identified by a stack-name and channel index
- SpecificAndRename() - Constructor for class org.anchoranalysis.plugin.image.task.bean.grouped.selectchannels.SpecificAndRename
- SpecificAxisBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.moments
-
A feature based one one-specific principal-axis as identified by image moments.
- SpecificAxisBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.moments.SpecificAxisBase
- SpecificDisabled - Class in org.anchoranalysis.io.output.bean.enabled
-
Only specific outputs, identified by a textual name, are disabled, and all others are enabled.
- SpecificDisabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
- SpecificDisabled(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificDisabled
- SpecificEnabled - Class in org.anchoranalysis.io.output.bean.enabled
-
Only specific outputs, identified by a textual name, are enabled.
- SpecificEnabled() - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
- SpecificEnabled(StringSet) - Constructor for class org.anchoranalysis.io.output.bean.enabled.SpecificEnabled
- SpecificEnergyChannelBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.energy
- SpecificEnergyChannelBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.energy.SpecificEnergyChannelBase
- Sphere - Class in org.anchoranalysis.mpp.mark.conic
-
A sphere
- Sphere() - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere
- Sphere(Bound) - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere
-
Creates with a radius within particular bounds.
- Sphere(Sphere) - Constructor for class org.anchoranalysis.mpp.mark.conic.Sphere
-
Copy Constructor
- split(Path) - Method in class org.anchoranalysis.bean.shared.path.RootPath
-
It splits the *root* portion of the path from the remainder
- split(Path, String, boolean) - Method in class org.anchoranalysis.plugin.io.input.path.RootPathMap
-
Given a path, it splits the *root* portion of the path from the remainder, trying a root identified by the rootName and debugMode (and if this fails, also trying with debugMode==false)
- SplitByObjects - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
- SplitByObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitByObjects
- SplitContourAtSaddlePoints - Class in org.anchoranalysis.plugin.points.bean.provider.object
-
Splits a 2D contour represented by an object-mask into several contours, splitting at "turn" points.
- SplitContourAtSaddlePoints() - Constructor for class org.anchoranalysis.plugin.points.bean.provider.object.SplitContourAtSaddlePoints
- SplitContourSmoothingSpline - Class in org.anchoranalysis.plugin.points.bean.contour
- SplitIntoSquares - Class in org.anchoranalysis.plugin.image.bean.object.provider.split
-
Splits objects into sub-objects by cutting by an orthogonal square lattice (like a chessboard).
- SplitIntoSquares() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.split.SplitIntoSquares
- SplitPath - Class in org.anchoranalysis.core.system.path
-
A path that has been split into two components: a root and a remainder.
- SplitPath(Path, Path) - Constructor for class org.anchoranalysis.core.system.path.SplitPath
- SQUARE_MICRO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
- SQUARE_NANO - org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
- stack() - Method in class org.anchoranalysis.mpp.io.input.MultiInput
- stack(String) - Static method in class org.anchoranalysis.plugin.image.provider.ReferenceFactory
- Stack - Class in org.anchoranalysis.image.core.stack
-
One ore more single-channel images that all have the same dimensions.
- Stack() - Constructor for class org.anchoranalysis.image.core.stack.Stack
- Stack(Stream<Channel>) - Constructor for class org.anchoranalysis.image.core.stack.Stack
- Stack(Channel) - Constructor for class org.anchoranalysis.image.core.stack.Stack
- Stack(Channel...) - Constructor for class org.anchoranalysis.image.core.stack.Stack
- Stack(Dimensions, ChannelFactorySingleType, int) - Constructor for class org.anchoranalysis.image.core.stack.Stack
- StackIdentifiers - Class in org.anchoranalysis.image.experiment.identifiers
- StackNotUniformSized - Class in org.anchoranalysis.image.core.stack
- StackNotUniformSized() - Constructor for class org.anchoranalysis.image.core.stack.StackNotUniformSized
- StackNotUniformSized(Stream<Channel>) - Constructor for class org.anchoranalysis.image.core.stack.StackNotUniformSized
- StackNotUniformSized(Channel) - Constructor for class org.anchoranalysis.image.core.stack.StackNotUniformSized
- StackProvider - Class in org.anchoranalysis.image.bean.provider.stack
- StackProvider() - Constructor for class org.anchoranalysis.image.bean.provider.stack.StackProvider
- StackProviderUnary - Class in org.anchoranalysis.image.bean.provider.stack
- StackProviderUnary() - Constructor for class org.anchoranalysis.image.bean.provider.stack.StackProviderUnary
- stacks() - Method in class org.anchoranalysis.annotation.io.AnnotationWithStrategy
- stacks() - Method in class org.anchoranalysis.image.bean.nonbean.init.ImageInitParams
- Stacks - Class in org.anchoranalysis.plugin.io.bean.input.stack
-
Each file gives either: * a single stack * a time-series of stacks
- Stacks() - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
- Stacks(InputManager<FileInput>) - Constructor for class org.anchoranalysis.plugin.io.bean.input.stack.Stacks
- STACKS - Static variable in class org.anchoranalysis.mpp.segment.define.OutputterDirectories
-
Where stacks are typically placed in a define-experiment output
- stackTrace() - Method in exception org.anchoranalysis.core.exception.friendly.AnchorFriendlyCheckedException
-
Prints a stack trace of the current exception to a string
- StackWithMap - Class in org.anchoranalysis.mpp.io.input
-
Combines a Stack with a map of other stacks
- StackWithMap(String, ProvidesStackInput) - Constructor for class org.anchoranalysis.mpp.io.input.StackWithMap
- standardDeviation() - Method in class org.anchoranalysis.math.histogram.Histogram
- StandardDeviation - Class in org.anchoranalysis.feature.bean.results
-
The standard-deviation of the results from a particular feature.
- StandardDeviation() - Constructor for class org.anchoranalysis.feature.bean.results.StandardDeviation
- start() - Method in class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
- start() - Method in class org.anchoranalysis.experiment.log.ConsoleMessageLogger
- start() - Method in class org.anchoranalysis.experiment.log.FailureOnlyMessageLogger
- start() - Method in class org.anchoranalysis.experiment.log.MessageLoggerList
- start() - Method in interface org.anchoranalysis.experiment.log.StatefulMessageLogger
- start() - Method in class org.anchoranalysis.experiment.log.TextFileMessageLogger
- start() - Method in class org.anchoranalysis.io.generator.text.TextFileOutput
- start() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
- start() - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack
-
Should always be called once before any calls to
ThumbnailFromStack.thumbnailFor(org.anchoranalysis.image.core.stack.Stack) - start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.DiscardOutliers
- start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.dependent.RelationWithMatches
- start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.GreaterIntersectionWith
- start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntensityGreaterEqualThan
- start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.IntersectsWith
- start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
- start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
- start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterPredicate
- start(Optional<Dimensions>, ObjectCollection) - Method in class org.anchoranalysis.plugin.image.bean.object.filter.ObjectFilterRelation
- start(FeatureInitParams, SharedFeatureMulti, Logger) - Method in class org.anchoranalysis.feature.session.SequentialSession
-
Starts the session
- start(EnergyStack) - Method in class org.anchoranalysis.mpp.feature.bean.mark.CheckMark
- start(EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.AndList
- start(EnergyStack) - Method in class org.anchoranalysis.plugin.mpp.bean.check.FeatureValueCheckMark
- start(ImageInitParams, Optional<EnergyStack>, Logger) - Method in interface org.anchoranalysis.image.feature.session.FeatureTableCalculator
-
Initializes a feature store that has the same structure as that previously created by createFeatures() from the same object
- start(ImageInitParams, Optional<EnergyStack>, Logger) - Method in class org.anchoranalysis.image.feature.session.merged.PairsTableCalculator
- start(ImageInitParams, Optional<EnergyStack>, Logger) - Method in class org.anchoranalysis.image.feature.session.SingleTableCalculator
- start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.OutlinePreserveRelativeSize
- start(ObjectCollection, StreamableCollection<BoundingBox>, Optional<Stack>) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.object.ThumbnailFromObjects
-
Initializes a batch to create thumbnails.
- start(FeedbackBeginParameters<T>) - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggregateTriggerBank
- startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
-
Derives a list of inputs from an object-collection
- startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
- startBatchDeriveInputs(ObjectCollection, EnergyStack, Logger) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
- startSeries(NoSharedState, NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.scale.ScaleImage
- startSeries(NoSharedState, OutputSequenceIndexed<Stack, String>, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.format.ConvertImageFormat
- startSeries(OutputSequenceIncrementing<Stack>, NoSharedState, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.bean.slice.MovieFromSlices
- startSeries(S, U, InputOutputContext) - Method in class org.anchoranalysis.image.experiment.bean.task.RasterTask
-
Starts processing of a series.
- StatefulMessageLogger - Interface in org.anchoranalysis.experiment.log
-
A
MessageLoggerthat can be started and stopped, and is aware this state. - StatefulNullMessageLogger - Class in org.anchoranalysis.experiment.bean.log
-
Does nothing (i.e.
- StatefulNullMessageLogger() - Constructor for class org.anchoranalysis.experiment.bean.log.StatefulNullMessageLogger
- stateReporter() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.AssignMode
- stateReporter() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.DirectAssignMode
- stateReporter() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- StateReporter<T,S> - Class in org.anchoranalysis.mpp.segment.bean.optimization
-
Converts the optimization state to a form that the reporter needs
- StateReporter() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.StateReporter
- StateReporterIdentity<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
Assumes the state is reported without any transformation
- StateReporterIdentity() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterIdentity
- StateReporterToPixelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
-
Assumes we are interested in
VoxelizedMarksWithEnergyas reporting type, and our optimization-state is in the formToPixelized<T> - StateReporterToPixelized() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterToPixelized
- StateReporterTransformer<T,S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter
- StateReporterTransformer() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.statereporter.StateReporterTransformer
- stateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridge
- stateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeIdentity
- stateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgePixelize
- stateToKernel() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.kernelbridge.KernelStateBridgeTransformer
- StateTransformer<W,X> - Interface in org.anchoranalysis.mpp.segment.transformer
- StateTransformerBean<S,T> - Class in org.anchoranalysis.mpp.segment.transformer
-
Transforms one type into another
- StateTransformerBean() - Constructor for class org.anchoranalysis.mpp.segment.transformer.StateTransformerBean
- StaticFilePath - Class in org.anchoranalysis.plugin.io.bean.filepath
- StaticFilePath() - Constructor for class org.anchoranalysis.plugin.io.bean.filepath.StaticFilePath
- StatisticalScoreBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.score
-
Calculates a score based upon the statistical mean and std-deviation.
- StatisticalScoreBase() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.score.StatisticalScoreBase
- StatisticForFeature - Class in org.anchoranalysis.feature.bean.results
-
Base class for calculating a statistic across all results in a
ResultsVectorListfor a particular feature. - StatisticForFeature() - Constructor for class org.anchoranalysis.feature.bean.results.StatisticForFeature
- statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Mean
- statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Quantile
- statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.StandardDeviation
- statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.StatisticForFeature
- statisticFromFeatureValue(DoubleArrayList) - Method in class org.anchoranalysis.feature.bean.results.Sum
- statisticsFor(int, int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
- statisticsForAllSlices(int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
- statisticsForAllSlices(VoxelizedMark, boolean) - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
- statisticsForAllSlicesMaskSlice(int, int, int) - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
- stdDev() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
- StdDev - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- StdDev() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.StdDev
- Steepest - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
- Steepest(SlidingBuffer<?>, WatershedEncoding, boolean, boolean, Optional<ObjectMask>) - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.Steepest
- steepestDescent(Point3i, int, int) - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.Steepest
- StoreSupplier<T> - Interface in org.anchoranalysis.core.identifier.provider.store
-
Supplier of an object for a store
- strategyForGrandchild() - Method in class org.anchoranalysis.feature.session.strategy.child.CheckCacheForSpecificChildren
- strategyForGrandchild() - Method in class org.anchoranalysis.feature.session.strategy.child.DefaultFindChildStrategy
- strategyForGrandchild() - Method in interface org.anchoranalysis.feature.session.strategy.child.FindChildStrategy
-
What strategy to use for children-of-children?
- stream() - Method in class org.anchoranalysis.core.functional.StreamableCollection
- stream() - Method in class org.anchoranalysis.core.identifier.provider.NameValueSet
- stream() - Method in class org.anchoranalysis.feature.results.ResultsVectorList
- stream() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
-
Provides various functional-programming operations on the object-collection
- stream() - Method in class org.anchoranalysis.spatial.box.BoundedList
-
A stream of elements in the list.
- StreamableCollection<T> - Class in org.anchoranalysis.core.functional
-
As a stream can only be used once, this data-structure allows for repeatedly getting streams from a collection
- StreamableCollection(Collection<T>) - Constructor for class org.anchoranalysis.core.functional.StreamableCollection
-
Create for a particular collection
- StreamableCollection(Supplier<Stream<T>>) - Constructor for class org.anchoranalysis.core.functional.StreamableCollection
- streamOverZ() - Method in class org.anchoranalysis.spatial.Extent
-
Streams over the range of z values
- streamStandardJava() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
-
A stream of object-masks as per Java's standard collections interface
- StringBeanCollection - Interface in org.anchoranalysis.bean
-
A bean that provides a collection of Strings.
- StringGenerator - Class in org.anchoranalysis.io.generator.text
- StringGenerator() - Constructor for class org.anchoranalysis.io.generator.text.StringGenerator
- StringList - Class in org.anchoranalysis.bean
-
A list of strings (order is defined).
- StringList() - Constructor for class org.anchoranalysis.bean.StringList
- StringListFactory - Class in org.anchoranalysis.bean.xml.factory
-
Creates a
StringListfrom a XML element. - StringListFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.StringListFactory
- StringMap - Class in org.anchoranalysis.bean.shared
- StringMap() - Constructor for class org.anchoranalysis.bean.shared.StringMap
- StringMapItem - Class in org.anchoranalysis.bean.shared
-
A simple mapping from one string (source) to another (target)
- StringMapItem() - Constructor for class org.anchoranalysis.bean.shared.StringMapItem
- stringRepresentationForElement(int) - Method in interface org.anchoranalysis.io.manifest.sequencetype.IncompleteElementRange
-
Returns the typed-index corresponding to the integer-index.
- StringSet - Class in org.anchoranalysis.bean
-
A set of strings.
- StringSet() - Constructor for class org.anchoranalysis.bean.StringSet
- StringSet(String...) - Constructor for class org.anchoranalysis.bean.StringSet
- StringSetFactory - Class in org.anchoranalysis.bean.xml.factory
-
Creates a
StringSetfrom a XML element. - StringSetFactory() - Constructor for class org.anchoranalysis.bean.xml.factory.StringSetFactory
- StringSuffixOutputNameStyle - Class in org.anchoranalysis.io.output.namestyle
- StringSuffixOutputNameStyle() - Constructor for class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
- StringSuffixOutputNameStyle(String, Optional<String>) - Constructor for class org.anchoranalysis.io.output.namestyle.StringSuffixOutputNameStyle
- StringsWithoutOrder - Class in org.anchoranalysis.io.manifest.sequencetype
-
A sequence of strings that has no order.
- StringsWithoutOrder() - Constructor for class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
- strMarks() - Method in class org.anchoranalysis.mpp.mark.conic.MarkWithPositionAndSingleRadius
- strPos() - Method in class org.anchoranalysis.mpp.mark.MarkWithPosition
- subdirectories() - Method in class org.anchoranalysis.io.manifest.directory.MutableDirectory
-
The
MutableDirectoryin the manifest for any subdirectories. - subdirectory(String, ManifestDirectoryDescription, boolean) - Method in interface org.anchoranalysis.io.output.outputter.InputOutputContext
-
Creates a new context that writes instead to a subdirectory.
- Subdirectory - Class in org.anchoranalysis.io.manifest.directory
-
A
SubdirectoryBaseentry in the manifest for a subdirectory. - Subdirectory() - Constructor for class org.anchoranalysis.io.manifest.directory.Subdirectory
- Subdirectory(Path) - Constructor for class org.anchoranalysis.io.manifest.directory.Subdirectory
- SubdirectoryBase - Class in org.anchoranalysis.io.manifest.directory
- SubdirectoryBase() - Constructor for class org.anchoranalysis.io.manifest.directory.SubdirectoryBase
- SubdirectoryBase(Path) - Constructor for class org.anchoranalysis.io.manifest.directory.SubdirectoryBase
- subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.GroupedStackBase
-
An optional subdirectory where the group outputs are placed.
- subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.histogram.ExportImageHistograms
- subdirectoryForGroupOutputs() - Method in class org.anchoranalysis.plugin.image.task.bean.grouped.raster.GroupedMeanChannelTask
- subList(int, int) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- SUBMARK_CORE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
- SUBMARK_CORE_INNER - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
- SUBMARK_INSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
- SUBMARK_OUTSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
- SUBMARK_SHELL - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
- SUBMARK_SHELL_OUTSIDE - Static variable in class org.anchoranalysis.mpp.mark.GlobalRegionIdentifiers
- SubmittedJob - Class in org.anchoranalysis.experiment.task.processor
- SubmittedJob(JobDescription, JobState) - Constructor for class org.anchoranalysis.experiment.task.processor.SubmittedJob
- subset(StringSet) - Method in class org.anchoranalysis.image.core.stack.NamedStacks
-
Creates a new collection containing only items whose keys exist in a particular set
- subsetCompatibleWith(Class<? extends FeatureInput>) - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
-
Extracts the subset of inputs that are compatible with a particular input-type
- subsetWhereBBoxIntersects(Dimensions, int, List<BoundingBox>) - Method in class org.anchoranalysis.mpp.mark.ColoredMarks
- subsetWhereBBoxIntersects(Dimensions, DrawOverlay, List<BoundingBox>) - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- subtract(int) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- subtract(VarianceCalculator) - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
- subtract(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.Extent
- subtract(ReadableTuple3i) - Method in class org.anchoranalysis.spatial.point.Tuple3i
- subtract(Tuple3d) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- subtractBackground(Channel, int, boolean) - Static method in class org.anchoranalysis.plugin.imagej.bean.channel.provider.BackgroundSubtractor
- subtractFrom(int) - Method in interface org.anchoranalysis.image.voxel.arithmetic.VoxelsArithmetic
-
Subtracts all current voxel-values from a constant-value
- SubtractFrom<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
- SubtractFrom() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.SubtractFrom
- SubtractFromConstant - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
- SubtractFromConstant() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractFromConstant
- subtractFromMaxValue() - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- SubtractMean - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
-
Subtract the mean (of the entire channel or a masked portion thereof) from every voxel
- SubtractMean() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractMean
- SubtractReducedFromMerged - Class in org.anchoranalysis.plugin.image.feature.bean.list.pair
-
Calculates
merged - reduce(first,second)for aFeatureInputPairObjects - SubtractReducedFromMerged() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.list.pair.SubtractReducedFromMerged
- SubtractSecondFromFirst - Class in org.anchoranalysis.image.feature.bean.object.pair
-
Subtract second-object from first-object in a pair
- SubtractSecondFromFirst() - Constructor for class org.anchoranalysis.image.feature.bean.object.pair.SubtractSecondFromFirst
- SubtractTwoChannels - Class in org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic
- SubtractTwoChannels(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.arithmetic.SubtractTwoChannels
- suffixStringForMeters(SpatialUnits.UnitSuffix) - Static method in class org.anchoranalysis.image.core.dimensions.SpatialUnits
-
A string that describes the suffix for meters.
- sum() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
- sum() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
- sum() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
- sum() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
- Sum<T extends FeatureInput> - Class in org.anchoranalysis.feature.bean.operator
- Sum - Class in org.anchoranalysis.feature.bean.results
-
The sum of the results from a particular feature.
- Sum - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- Sum() - Constructor for class org.anchoranalysis.feature.bean.operator.Sum
- Sum() - Constructor for class org.anchoranalysis.feature.bean.results.Sum
- Sum() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Sum
- Sum(FeatureList<T>) - Constructor for class org.anchoranalysis.feature.bean.operator.Sum
- sumBuffer() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
- summarize() - Method in exception org.anchoranalysis.bean.xml.error.BeanMisconfiguredXmlException
-
This summarize() option just looks for the most deep exception that can be 'combined' and takes its message
- summarize() - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
- summarize() - Method in exception org.anchoranalysis.core.exception.combinable.AnchorCombinableException
- summarize() - Method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
- SummarizeBase<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.task
- SummarizeBase() - Constructor for class org.anchoranalysis.plugin.io.bean.task.SummarizeBase
- summarizeDisabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
-
A comma-separated string of all output-names that were not enabled.
- summarizeEnabled() - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
-
A comma-separated string of all output-names that were enabled.
- summarizeIgnoreIdenticalFilePath(Path) - Method in exception org.anchoranalysis.bean.xml.error.LocalisedBeanException
-
If there is no nested-set of combinable exceptions, and the filenameDscr related to this current exception, is identical as the passed parameter, then we simply ignore the LocalisedBean and promote its getCause()
- SummarizeInputs<T extends InputFromManager> - Class in org.anchoranalysis.plugin.io.bean.task
- SummarizeInputs() - Constructor for class org.anchoranalysis.plugin.io.bean.task.SummarizeInputs
- summarizeMultiplex(boolean) - Method in class org.anchoranalysis.io.output.recorded.RecordedOutputs
-
Multiplex between
RecordedOutputs.summarizeEnabled()andRecordedOutputs.summarizeDisabled(). - Summarizer<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Summarizes a set of elements by outputting a descriptive string
- Summarizer() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.Summarizer
- SummarizerAggregate<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Collects summary data about a set of input files that will eventually be outputted to the user
- SummarizerAggregate() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerAggregate
- SummarizerCount<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
A count of the number of inputs.
- SummarizerCount() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerCount
- SummarizerInputFromManager<T extends InputFromManager,S> - Class in org.anchoranalysis.plugin.io.bean.summarizer.input
-
Extracts a particular item from an InputManager for summarization downstream
- SummarizerInputFromManager() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.input.SummarizerInputFromManager
- SummarizerListMultiline<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Creates a string where each line is an element (the string representation thereof)
- SummarizerListMultiline() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerListMultiline
- SummarizerNamedChannels<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
-
Summarzes
NamedChannelsInputin different ways - SummarizerNamedChannels() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannels
- SummarizerNamedChannelsSimple<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer.image
-
A simple summerizer where there's one summary-item per image (series are ignored!)
- SummarizerNamedChannelsSimple() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.image.SummarizerNamedChannelsSimple
- SummarizerSplitMoreThan<T> - Class in org.anchoranalysis.plugin.io.bean.summarizer
-
Multiplexes between two summarizers depending on the total number of count
- SummarizerSplitMoreThan() - Constructor for class org.anchoranalysis.plugin.io.bean.summarizer.SummarizerSplitMoreThan
- SummaryException - Exception in org.anchoranalysis.core.exception.combinable
-
A special kind of exception that represents a summary of an existing set of exceptions
- SummaryException(String, Throwable) - Constructor for exception org.anchoranalysis.core.exception.combinable.SummaryException
- summaryStr() - Method in class org.anchoranalysis.spatial.Contour
- sumNonZero() - Method in class org.anchoranalysis.math.histogram.Histogram
- sumOfSquares() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
- sumOfSquares() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
- sumOfSquares() - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
- sumOverlapFromPaired() - Method in class org.anchoranalysis.annotation.io.assignment.AssignmentOverlapFromPairs
- SupportsTimeSeries - Class in org.anchoranalysis.io.imagej.bean.stack.writer
-
Base class for
ImageJRasterWriterthat does support writing time-series as a stack. - SupportsTimeSeries() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.SupportsTimeSeries
- suppressedLogErrorReporter() - Static method in class org.anchoranalysis.test.LoggingFixture
-
A
Loggerthat doesn't output anything - suppressedLogReporter() - Static method in class org.anchoranalysis.test.LoggingFixture
-
A
MessageLoggerthat doesn't output anything - SuppressNonMaxima<T> - Class in org.anchoranalysis.plugin.opencv.bean.object.segment.stack
-
Applies a segmentation procedure followed by non-maxima suppression.
- SuppressNonMaxima() - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
- SuppressNonMaxima(SegmentStackIntoObjectsPooled<T>) - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
-
Creates with a particular segmentation algorithm as an input.
- SuppressNonMaxima(SegmentStackIntoObjectsPooled<T>, ReduceElements<ObjectMask>) - Constructor for class org.anchoranalysis.plugin.opencv.bean.object.segment.stack.SuppressNonMaxima
- SurfaceNumberVoxelFaces - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
The number of voxel-faces along the surface (the faces of each voxel that touch outside)
- SurfaceNumberVoxelFaces() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelFaces
- SurfaceNumberVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
-
The number of voxels on the surface (all voxels on the exterior of the object)
- SurfaceNumberVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxels
- SurfaceNumberVoxelsBase - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.surface
- SurfaceNumberVoxelsBase() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.surface.SurfaceNumberVoxelsBase
- SurfaceSizeMaskNonZero - Class in org.anchoranalysis.plugin.mpp.feature.bean.memo.ind
- SurfaceSizeMaskNonZero() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.memo.ind.SurfaceSizeMaskNonZero
- SwitchChannelTime - Class in org.anchoranalysis.io.bioformats.bean.options
-
Treats the channel index as if it's time, and vice versa
- SwitchChannelTime() - Constructor for class org.anchoranalysis.io.bioformats.bean.options.SwitchChannelTime
- SwitchDetailedLogging - Class in org.anchoranalysis.experiment.bean.log
-
Switches between two log-reporters depending on whether detailed logging is switched on or not
- SwitchDetailedLogging() - Constructor for class org.anchoranalysis.experiment.bean.log.SwitchDetailedLogging
T
- TableItemArrangement<T> - Class in org.anchoranalysis.image.bean.nonbean.spatial.arrange
- TableItemArrangement(TableItemArrangement.TableCreator<T>, int, int) - Constructor for class org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemArrangement
- TableItemArrangement.TableCreator<T> - Interface in org.anchoranalysis.image.bean.nonbean.spatial.arrange
- TableItemException - Exception in org.anchoranalysis.image.bean.nonbean.spatial.arrange
- TableItemException(Exception) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemException
- TableItemException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.spatial.arrange.TableItemException
- tail() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
- Task<T extends InputFromManager,S> - Class in org.anchoranalysis.experiment.bean.task
-
A task which performs some kind of processing on a specific input-object
- Task() - Constructor for class org.anchoranalysis.experiment.bean.task.Task
- TaskFactory - Class in org.anchoranalysis.launcher.executor.selectparam.task
-
A factory that creates
SelectParam<Optional<Path>>as required for tasks. - TaskStatistics - Class in org.anchoranalysis.experiment.task
-
Maintains statistics on the execution of a task (considering jobs in aggregate)
- TaskStatistics(long, RunningSum, RunningSum) - Constructor for class org.anchoranalysis.experiment.task.TaskStatistics
- TaskWithoutSharedState<T extends InputFromManager> - Class in org.anchoranalysis.experiment.bean.task
-
A particular type of task that doesn't share-state between running jobs
- TaskWithoutSharedState() - Constructor for class org.anchoranalysis.experiment.bean.task.TaskWithoutSharedState
- TerminationCondition - Class in org.anchoranalysis.mpp.segment.bean.optimization.termination
-
A test on whether to terminate the optimization or not
- TerminationCondition() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationCondition
- TerminationConditionListOr - Class in org.anchoranalysis.mpp.segment.bean.optimization.termination
- TerminationConditionListOr() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
- TerminationConditionListOr(TerminationCondition, TerminationCondition) - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.termination.TerminationConditionListOr
- test(byte, byte) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.PredicateTwoBytes
-
Do the combination of two arguments fulfill the predicate?
- test(Point3i, T, T, int, int) - Method in interface org.anchoranalysis.image.voxel.iterator.predicate.buffer.PredicateBufferBinary
-
Tests a voxel location in two buffers
- test(T) - Method in interface org.anchoranalysis.core.functional.checked.CheckedPredicate
-
Applies a predicate like with
Predicate.test(T). - TestDataInitException - Exception in org.anchoranalysis.test
-
An exception thrown when test-data cannot be loaded
- TestDataInitException(String) - Constructor for exception org.anchoranalysis.test.TestDataInitException
- TestDataInitException(Throwable) - Constructor for exception org.anchoranalysis.test.TestDataInitException
- TestDataLoadException - Exception in org.anchoranalysis.test
-
An exception thrown when test-data cannot be loaded
- TestDataLoadException(String) - Constructor for exception org.anchoranalysis.test.TestDataLoadException
- TestDataLoadException(Throwable) - Constructor for exception org.anchoranalysis.test.TestDataLoadException
- TestLoader - Class in org.anchoranalysis.test
-
Loads test data, which is found at some location on the filesystem
- TestLoaderMPP - Class in org.anchoranalysis.test.experiment
- TestLoaderMPP(TestLoader) - Constructor for class org.anchoranalysis.test.experiment.TestLoaderMPP
- testManifestExperiment(String) - Method in class org.anchoranalysis.test.TestLoader
- textColor() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
- textColor() - Method in class org.anchoranalysis.core.color.RGBColor
- TextFile - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- TextFile() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFile
- TextFileAsIntegerFromManifest - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
- TextFileAsIntegerFromManifest() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.TextFileAsIntegerFromManifest
- TextFileAsIntegerFromPath - Class in org.anchoranalysis.plugin.mpp.experiment.bean.feature.report
- TextFileAsIntegerFromPath() - Constructor for class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.TextFileAsIntegerFromPath
- TextFileMarksReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- TextFileMarksReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TextFileMarksReporter
- TextFileMessageLogger - Class in org.anchoranalysis.experiment.log
-
Logs messages to a text-file.
- TextFileMessageLogger(String, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.log.TextFileMessageLogger
-
Constructs a logger that (always) writes messages to a text-file with a specific path.
- TextFileMessageLogger(String, OutputterChecked, ErrorReporter) - Constructor for class org.anchoranalysis.experiment.log.TextFileMessageLogger
-
Constructs a logger that (maybe) writes messages to a text-file, with a path based upon an output name applied to a
OutputterChecked. - TextFileOutput - Class in org.anchoranalysis.io.generator.text
-
Utility for writing to a text-file at a particular path, but only if it is enabled.
- TextFileOutput(String) - Constructor for class org.anchoranalysis.io.generator.text.TextFileOutput
- TextFileOutputter - Class in org.anchoranalysis.io.generator.text
-
Maybe creates a
TextFileOutputbased upon settings in aOutputterChecked. - TextFileReader - Class in org.anchoranalysis.io.manifest.file
- TextureScore - Class in org.anchoranalysis.plugin.image.feature.bean.object.single.intensity
-
From Page 727 from Lin et al (A Multi-Model Approach to Simultaneous Segmentation and Classification of Heterogeneous Populations of Cell Nuclei
- TextureScore() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.single.intensity.TextureScore
- ThreeChannels - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
- ThreeChannels() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeChannels
- ThreeColoredObjects - Class in org.anchoranalysis.plugin.image.bean.stack.provider.color
-
Colors three collections of objects in RED, GREEN, BLUE channels on top of a background.
- ThreeColoredObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.stack.provider.color.ThreeColoredObjects
- ThreeWayBranchXYResolution - Class in org.anchoranalysis.plugin.io.bean.stack.reader
-
Takes the XY-resolution determined by stackReaderInput.
- ThreeWayBranchXYResolution() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.reader.ThreeWayBranchXYResolution
- threshold() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- threshold() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToThreshold
-
The threshold-value
- threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOffVoxels
- threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryNotOnVoxels
- threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOffVoxels
- threshold() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryOnVoxels
- threshold(RelationToThreshold) - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
- threshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
- threshold(RelationToThreshold) - Method in class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
- threshold(VoxelsWrapper) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder
-
Like
Thresholder.threshold(VoxelsWrapper)but using default binary-values. - threshold(VoxelsWrapper, BinaryValuesByte) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder
-
Like
Thresholder.threshold(VoxelsWrapper, BinaryValuesByte, Optional, Optional)applying the thresholding to the entire set of voxels. - threshold(VoxelsWrapper, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.threshold.Thresholder
-
Thresholds voxels (across a range of values) so that they have only binary range (i.e.
- threshold(VoxelsWrapper, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
- threshold(VoxelsWrapper, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
- threshold(VoxelsWrapper, BinaryValuesByte, Optional<Histogram>, Optional<ObjectMask>) - Method in class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
- threshold(RelationToValue, double) - Method in class org.anchoranalysis.math.histogram.Histogram
- Threshold - Class in org.anchoranalysis.plugin.image.bean.mask.provider.segment
-
Thresholds a channel to produce a mask, reusing (and modifying) the input-buffers of the channel if possible.
- Threshold() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.segment.Threshold
- ThresholdAgainstChannel - Class in org.anchoranalysis.plugin.image.bean.segment.binary
-
Thresholds each voxels by comparing against another channel that has per-voxel thresholds
- ThresholdAgainstChannel() - Constructor for class org.anchoranalysis.plugin.image.bean.segment.binary.ThresholdAgainstChannel
- ThresholdConfidence - Class in org.anchoranalysis.plugin.image.bean.object.segment.reduce
-
Combines object-masks by projecting the maximum confidence-level for each voxel and thresholding.
- ThresholdConfidence() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
- ThresholdConfidence(double) - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.reduce.ThresholdConfidence
-
Creates with a minimum-confidence level.
- Thresholded - Class in org.anchoranalysis.plugin.mpp.bean.region
- Thresholded() - Constructor for class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
- ThresholdedFeature - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Only keeps objects whose feature-value satisfies a condition relative to a threshold.
- ThresholdedFeature() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedFeature
- ThresholdedVolume - Class in org.anchoranalysis.plugin.image.bean.object.filter.independent
-
Only keeps objects whose feature-value satisfies a condition relative to a threshold.
- ThresholdedVolume() - Constructor for class org.anchoranalysis.plugin.image.bean.object.filter.independent.ThresholdedVolume
- Thresholder - Class in org.anchoranalysis.image.bean.threshold
-
Thresholds a voxels to create a binary-voxels
- Thresholder() - Constructor for class org.anchoranalysis.image.bean.threshold.Thresholder
- ThresholderAutoIJ - Class in org.anchoranalysis.plugin.fiji.bean.threshold
- ThresholderAutoIJ() - Constructor for class org.anchoranalysis.plugin.fiji.bean.threshold.ThresholderAutoIJ
- ThresholderGlobal - Class in org.anchoranalysis.image.bean.threshold
-
Performs global thresholding.
- ThresholderGlobal() - Constructor for class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
- ThresholderGlobal(CalculateLevel) - Constructor for class org.anchoranalysis.image.bean.threshold.ThresholderGlobal
- ThresholderSimpleFillHoles2D - Class in org.anchoranalysis.plugin.imagej.bean.threshold
- ThresholderSimpleFillHoles2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
- ThresholderSimpleFillHoles2D(int) - Constructor for class org.anchoranalysis.plugin.imagej.bean.threshold.ThresholderSimpleFillHoles2D
- thresholdForLevel(Voxels<UnsignedByteBuffer>, int, BinaryValuesByte) - Static method in class org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder
- thresholdForLevel(VoxelsWrapper, int, BinaryValuesByte, Optional<ObjectMask>, boolean) - Static method in class org.anchoranalysis.image.voxel.thresholder.VoxelsThresholder
- ThresholdHistogram - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.threshold
-
Thresholds the histogram (using a weightedOtsu) and then applies a feature to the thresholded version
- ThresholdHistogram() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.threshold.ThresholdHistogram
- ThumbnailBatch<T> - Interface in org.anchoranalysis.plugin.image.thumbnail
-
Creates thumbnails for a particular batch of objects that can be calibrated to have similar properties (identical scale etc.)
- thumbnailFor(Stack) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ScaleToSize
- thumbnailFor(Stack) - Method in class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack
-
Creates a thumbnail for a stack
- thumbnailFor(T) - Method in interface org.anchoranalysis.plugin.image.thumbnail.ThumbnailBatch
-
Creates a thumbnail for an element in the batch
- ThumbnailFromObjects - Class in org.anchoranalysis.plugin.image.bean.thumbnail.object
-
Creates a thumbnail of one or more objects on a stack by drawing the outline of the objects
- ThumbnailFromObjects() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.object.ThumbnailFromObjects
- ThumbnailFromStack - Class in org.anchoranalysis.plugin.image.bean.thumbnail.stack
-
Creates a thumbnail from a stack
- ThumbnailFromStack() - Constructor for class org.anchoranalysis.plugin.image.bean.thumbnail.stack.ThumbnailFromStack
- Tiff - Class in org.anchoranalysis.io.imagej.bean.stack.writer
-
Writes a TIFF image using ImageJ.
- Tiff - Class in org.anchoranalysis.plugin.io.bean.stack.writer.bioformats
-
Writes a stack to the filesystem as a TIFF using the Bioformats library.
- Tiff() - Constructor for class org.anchoranalysis.io.imagej.bean.stack.writer.Tiff
- Tiff() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.Tiff
- TiffTimeSeries - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- TiffTimeSeries() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.TiffTimeSeries
- Tile - Class in org.anchoranalysis.image.bean.spatial.arrange
- Tile() - Constructor for class org.anchoranalysis.image.bean.spatial.arrange.Tile
- TimeSequence - Class in org.anchoranalysis.image.core.stack
- TimeSequence() - Constructor for class org.anchoranalysis.image.core.stack.TimeSequence
- TimeSequence(Stack) - Constructor for class org.anchoranalysis.image.core.stack.TimeSequence
- title() - Method in class org.anchoranalysis.io.output.bean.ReportFeature
- title() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureEvaluator
- title() - Method in class org.anchoranalysis.mpp.io.bean.report.feature.ReportFeatureWrapError
- title() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.NumberMarksFromManifest
- title() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.ReportFeatureForManifestFileBase
- title() - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.feature.report.RootFilePathRegEx
- toAll() - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
-
Assigns to all the voxels
- toArray() - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- toArray(T[]) - Method in class org.anchoranalysis.mpp.feature.mark.ListUpdatableMarkSetCollection
- toAWTColor() - Method in class org.anchoranalysis.bean.shared.color.RGBColorBean
- toAWTColor() - Method in class org.anchoranalysis.core.color.RGBColor
- toBox(BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
-
Assigns to only voxels inside a bounding-box
- ToByte - Class in org.anchoranalysis.image.voxel.convert
-
Base class for conversion to unsigned 8-bit.
- ToByte - Class in org.anchoranalysis.plugin.image.bean.channel.convert
- ToByte() - Constructor for class org.anchoranalysis.image.voxel.convert.ToByte
- ToByte() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.ToByte
- ToByteNoScaling - Class in org.anchoranalysis.image.voxel.convert
-
Converts voxel buffers to a unsigned 8-bit buffer without scaling any values.
- ToByteNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToByteNoScaling
- ToByteScaleByMaxValue - Class in org.anchoranalysis.image.voxel.convert
-
Converts voxel buffers to a unsigned 8-bit buffer linearly scaling against the maximum constant value.
- ToByteScaleByMaxValue(int) - Constructor for class org.anchoranalysis.image.voxel.convert.ToByteScaleByMaxValue
- ToByteScaleByMinMaxValue - Class in org.anchoranalysis.image.voxel.convert
-
Converts voxel buffers to a unsigned 8-bit buffer scaling against a the minimum and maximum constant.
- ToByteScaleByMinMaxValue(int, int) - Constructor for class org.anchoranalysis.image.voxel.convert.ToByteScaleByMinMaxValue
- ToByteScaleByType - Class in org.anchoranalysis.image.voxel.convert
-
Converts voxel buffers to a
UnsignedByteBufferscaling against the maximum value in each buffer. - ToByteScaleByType() - Constructor for class org.anchoranalysis.image.voxel.convert.ToByteScaleByType
- ToByteUpperLowerQuantileIntensity - Class in org.anchoranalysis.plugin.image.bean.channel.convert.histogram
- ToByteUpperLowerQuantileIntensity() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.convert.histogram.ToByteUpperLowerQuantileIntensity
- toChannel(ImagePlus, Optional<Resolution>) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertFromImagePlus
-
Converts an
ImagePlusto aChannel. - toCommandLineException() - Method in exception org.anchoranalysis.launcher.executor.selectparam.path.InvalidPathArgumentException
- ToConsole - Class in org.anchoranalysis.experiment.bean.log
-
Logs messages to the console.
- ToConsole() - Constructor for class org.anchoranalysis.experiment.bean.log.ToConsole
- toEitherTwoObjects(ObjectMask, ObjectMask, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
-
Sets voxels to a value if the position is ON in either of two masks
- toExtent() - Method in class org.anchoranalysis.plugin.io.multifile.SizeExtents
- toFloat() - Method in class org.anchoranalysis.spatial.point.Point2d
- ToFloat - Class in org.anchoranalysis.image.core.channel.convert
- ToFloat - Class in org.anchoranalysis.io.bioformats.copyconvert.tofloat
- ToFloat() - Constructor for class org.anchoranalysis.image.core.channel.convert.ToFloat
- ToFloat() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tofloat.ToFloat
- ToFloatNoScaling - Class in org.anchoranalysis.image.voxel.convert
-
Converts voxel buffers to a
FloatBufferwithout scaling any values. - ToFloatNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToFloatNoScaling
- ToInt - Class in org.anchoranalysis.io.bioformats.copyconvert.toint
- ToInt() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toint.ToInt
- ToMultiple - Class in org.anchoranalysis.experiment.bean.log
-
Rather than logging to one location, logs to multiple locations (from a list).
- ToMultiple() - Constructor for class org.anchoranalysis.experiment.bean.log.ToMultiple
- ToMultiple(LoggingDestination, LoggingDestination) - Constructor for class org.anchoranalysis.experiment.bean.log.ToMultiple
-
Constructs a logger to two locations
- toObject(ObjectMask) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
-
Sets voxels in a box to a particular value if they match an object-mask
- toObject(ObjectMask, BoundingBox) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
-
Sets voxels in a box to a particular value if they match a object-mask (but only a part of the object-mask)
- toObjectIf(ObjectMask, IntPredicate) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
-
Sets voxels in a box to a particular value if they match an object-mask and a voxel matches a predicate
- toObjectWhile(ObjectMask, IntPredicate) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
-
Sets voxels in a box to a particular value if they match an object-mask and each voxel matches a predicate
- toPhysicalArea(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
-
Converts an area from square voxels to square meters.
- toPhysicalArea(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
-
Converts an area from square voxels to physical units.
- toPhysicalDistance(double, DirectionVector) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
-
Converts a distance from voxels to meters.
- toPhysicalDistance(double, DirectionVector, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
-
Converts a distance from voxels to physical units.
- toPhysicalVolume(double) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
-
Converts a volume from cubic voxels to cubic meters.
- toPhysicalVolume(double, String) - Method in class org.anchoranalysis.image.core.dimensions.UnitConverter
-
Converts a volume from cubic voxels to physical units.
- ToPixelized<T> - Class in org.anchoranalysis.plugin.mpp.segment.optimization
-
Before and after state, when a
srcis coverted in aVoxelizedMarksWithEnergy - ToPixelized(T, VoxelizedMarksWithEnergy) - Constructor for class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
- ToPixelizedExtracter<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract
- ToPixelizedExtracter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.extract.ToPixelizedExtracter
- toSet() - Method in class org.anchoranalysis.image.voxel.object.ObjectMaskStream
-
Converts to a
HashSet(newly-created). - ToShortNoScaling - Class in org.anchoranalysis.image.voxel.convert
-
Converts voxel buffers to a unsigned 16-bit buffer without scaling any values.
- ToShortNoScaling() - Constructor for class org.anchoranalysis.image.voxel.convert.ToShortNoScaling
- ToShortScaleByType - Class in org.anchoranalysis.image.voxel.convert
-
Converts voxel buffers to a unsigned 16-bit buffer, scaling against the maximum value in each data-type.
- ToShortScaleByType() - Constructor for class org.anchoranalysis.image.voxel.convert.ToShortScaleByType
- toStack(Mat) - Static method in class org.anchoranalysis.plugin.opencv.convert.ConvertFromMat
- toString() - Method in class org.anchoranalysis.annotation.image.ImageLabelAnnotation
- toString() - Method in class org.anchoranalysis.annotation.io.assignment.CostMatrix
- toString() - Method in class org.anchoranalysis.annotation.io.image.findable.Found
- toString() - Method in class org.anchoranalysis.annotation.io.image.findable.NotFound
- toString() - Method in class org.anchoranalysis.bean.AnchorBean
-
By default, we use
AnchorBean.describeBean()as the string representation of the bean. - toString() - Method in class org.anchoranalysis.bean.initializable.property.SimplePropertyDefiner
- toString() - Method in class org.anchoranalysis.bean.NamedBean
- toString() - Method in class org.anchoranalysis.bean.shared.regex.RegExList
- toString() - Method in class org.anchoranalysis.bean.shared.regex.RegExSimple
- toString() - Method in class org.anchoranalysis.bean.shared.relation.EqualToBean
- toString() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanBean
- toString() - Method in class org.anchoranalysis.bean.shared.relation.GreaterThanEqualToBean
- toString() - Method in class org.anchoranalysis.bean.shared.relation.LessThanBean
- toString() - Method in class org.anchoranalysis.bean.shared.relation.LessThanEqualToBean
- toString() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
- toString() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- toString() - Method in class org.anchoranalysis.core.color.RGBColor
- toString() - Method in exception org.anchoranalysis.core.exception.AnchorRuntimeException
- toString() - Method in class org.anchoranalysis.core.graph.GraphWithoutPayload
- toString() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
- toString() - Method in class org.anchoranalysis.core.graph.TypedEdge
- toString() - Method in class org.anchoranalysis.core.identifier.getter.IdentifierModulo
- toString() - Method in class org.anchoranalysis.core.log.CommonContext
- toString() - Method in class org.anchoranalysis.core.system.path.SplitPath
- toString() - Method in class org.anchoranalysis.core.value.TypedValue
- toString() - Method in class org.anchoranalysis.experiment.task.InputTypesExpected
- toString() - Method in class org.anchoranalysis.experiment.task.ParametersUnbound
- toString() - Method in class org.anchoranalysis.experiment.task.processor.JobDescription
- toString() - Method in class org.anchoranalysis.feature.bean.Feature
- toString() - Method in class org.anchoranalysis.feature.calculate.cache.ChildCacheName
- toString() - Method in class org.anchoranalysis.feature.calculate.FeatureInitParams
- toString() - Method in class org.anchoranalysis.feature.energy.EnergyTotal
- toString() - Method in class org.anchoranalysis.feature.input.FeatureInputResults
- toString() - Method in class org.anchoranalysis.feature.io.csv.FeatureCSVMetadata
- toString() - Method in class org.anchoranalysis.feature.io.name.CombinedName
- toString() - Method in interface org.anchoranalysis.feature.io.name.MultiName
-
The full name, including both directory and file part, as a string.
- toString() - Method in class org.anchoranalysis.feature.io.name.SimpleName
- toString() - Method in class org.anchoranalysis.feature.name.FeatureNameList
- toString() - Method in class org.anchoranalysis.feature.results.ResultsVector
- toString() - Method in class org.anchoranalysis.feature.shared.SharedFeatureMulti
- toString() - Method in class org.anchoranalysis.image.bean.nonbean.spatial.arrange.BoundingBoxesOnPlane
- toString() - Method in class org.anchoranalysis.image.bean.spatial.SizeXY
- toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPhysical
- toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.area.AreaPixels
- toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
- toString() - Method in class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
- toString() - Method in class org.anchoranalysis.image.core.channel.Channel
-
Display a histogram of voxel-intensities as the string-representation
- toString() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- toString() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- toString() - Method in class org.anchoranalysis.image.core.mask.Mask
- toString() - Method in class org.anchoranalysis.image.core.object.label.OverlappingObject
- toString() - Method in class org.anchoranalysis.image.core.object.MatchedObject
- toString() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
- toString() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- toString() - Method in class org.anchoranalysis.image.core.orientation.Orientation2D
- toString() - Method in class org.anchoranalysis.image.core.orientation.Orientation3DEulerAngles
- toString() - Method in class org.anchoranalysis.image.core.orientation.OrientationAxisAngle
- toString() - Method in class org.anchoranalysis.image.core.outline.traverser.path.ContiguousVoxelPath
- toString() - Method in class org.anchoranalysis.image.core.outline.traverser.path.DistanceIndex
- toString() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.LoopablePoints
- toString() - Method in class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
- toString() - Method in class org.anchoranalysis.image.feature.evaluator.NamedFeatureCalculatorMulti
- toString() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputPairObjects
- toString() - Method in class org.anchoranalysis.image.feature.object.input.FeatureInputSingleObject
- toString() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
- toString() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
- toString() - Method in class org.anchoranalysis.image.voxel.datatype.VoxelDataType
- toString() - Method in class org.anchoranalysis.image.voxel.kernel.outline.OutlineKernelParameters
- toString() - Method in class org.anchoranalysis.image.voxel.neighborhood.EdgeAdderParameters
- toString() - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
-
Default string representation of the collection, one line with each object described by its center-of-gravity
- toString() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
-
A string representation of the object-mask showing: the center-of-gravity the number of "ON" voxels on the object
- toString() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
- toString() - Method in class org.anchoranalysis.io.generator.combined.OptionalNameValue
- toString() - Method in class org.anchoranalysis.io.generator.sequence.BoundOutputter
- toString() - Method in class org.anchoranalysis.io.manifest.file.FileType
- toString() - Method in class org.anchoranalysis.io.manifest.ManifestDescription
- toString() - Method in class org.anchoranalysis.io.output.outputter.directory.OutputterTarget
- toString() - Method in class org.anchoranalysis.io.output.outputter.Outputter
- toString() - Method in class org.anchoranalysis.io.output.path.prefixer.NamedPath
- toString() - Method in class org.anchoranalysis.launcher.config.HelpConfig
- toString() - Method in class org.anchoranalysis.math.histogram.Histogram
- toString() - Method in class org.anchoranalysis.math.moment.EigenvalueAndVector
- toString() - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
- toString() - Method in class org.anchoranalysis.mpp.bean.bound.ResolvedBound
- toString() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembership
- toString() - Method in class org.anchoranalysis.mpp.bean.regionmap.RegionMembershipWithFlags
- toString() - Method in class org.anchoranalysis.mpp.bound.BidirectionalBound
- toString() - Method in class org.anchoranalysis.mpp.feature.energy.EnergyPair
- toString() - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- toString() - Method in class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- toString() - Method in class org.anchoranalysis.mpp.feature.energy.saved.EnergySavedPairs
- toString() - Method in class org.anchoranalysis.mpp.feature.input.memo.FeatureInputPairMemo
- toString() - Method in class org.anchoranalysis.mpp.io.marks.ColoredMarksWithDisplayStack
- toString() - Method in class org.anchoranalysis.mpp.io.marks.MarksWithDisplayStack
- toString() - Method in class org.anchoranalysis.mpp.mark.conic.Circle
- toString() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- toString() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- toString() - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
- toString() - Method in class org.anchoranalysis.mpp.mark.Mark
-
String representation of the mark
- toString() - Method in class org.anchoranalysis.mpp.mark.MarkCollection
- toString() - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- toString() - Method in class org.anchoranalysis.mpp.mark.points.PointList
- toString() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
- toString() - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
- toString() - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
- toString() - Method in class org.anchoranalysis.mpp.pair.IdentifiablePair
- toString() - Method in class org.anchoranalysis.mpp.pair.PairPxlMarkMemo
- toString() - Method in class org.anchoranalysis.mpp.proposer.error.ErrorNodeImpl
- toString() - Method in class org.anchoranalysis.mpp.proposer.ProposerContext
- toString() - Method in class org.anchoranalysis.mpp.segment.bean.kernel.proposer.KernelProposer
- toString() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.KernelWithIdentifier
- toString() - Method in class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
- toString() - Method in class org.anchoranalysis.mpp.segment.optimization.DualStack
- toString() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.AggIDCounter
- toString() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.aggregate.Aggregator
- toString() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackBeginParameters
- toString() - Method in class org.anchoranalysis.mpp.segment.optimization.feedback.FeedbackEndParameters
- toString() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- toString() - Method in class org.anchoranalysis.overlay.writer.ObjectDrawAttributes
- toString() - Method in class org.anchoranalysis.plot.AxisLimits
- toString() - Method in class org.anchoranalysis.plugin.annotation.comparison.AnnotationComparisonInput
- toString() - Method in class org.anchoranalysis.plugin.annotation.comparison.ObjectsToCompare
- toString() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateObjectMask
- toString() - Method in class org.anchoranalysis.plugin.image.feature.object.calculation.single.CalculateShellObjectMask
- toString() - Method in class org.anchoranalysis.plugin.image.object.merge.ObjectVertex
- toString() - Method in class org.anchoranalysis.plugin.image.task.bean.format.ChangeableOutputSequence
- toString() - Method in class org.anchoranalysis.plugin.image.task.feature.InitParamsWithEnergyStack
- toString() - Method in class org.anchoranalysis.plugin.image.task.feature.ResultsVectorWithThumbnail
- toString() - Method in class org.anchoranalysis.plugin.image.task.grouped.NamedChannel
- toString() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageCSVLabellerInitParams
- toString() - Method in class org.anchoranalysis.plugin.image.task.labeller.ImageLabellerStringMapInitParams
- toString() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- toString() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
- toString() - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelDeath.MarkAnd
- toString() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.PartitionedMarks
- toString() - Method in class org.anchoranalysis.plugin.mpp.segment.optimization.ToPixelized
- toString() - Method in class org.anchoranalysis.plugin.points.bean.fitter.FitResult
- toString() - Method in class org.anchoranalysis.plugin.points.calculate.ellipse.ObjectWithEllipse
- toString() - Method in class org.anchoranalysis.plugin.points.contour.ContourList
- toString() - Method in class org.anchoranalysis.spatial.box.BoundingBox
- toString() - Method in class org.anchoranalysis.spatial.Extent
- toString() - Method in class org.anchoranalysis.spatial.point.Point2d
- toString() - Method in class org.anchoranalysis.spatial.point.Point2f
- toString() - Method in class org.anchoranalysis.spatial.point.Point2i
- toString() - Method in class org.anchoranalysis.spatial.point.Tuple3d
- toString() - Method in class org.anchoranalysis.spatial.point.Tuple3f
- toString() - Method in class org.anchoranalysis.spatial.point.Tuple3i
- toString() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
- toString() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
- toString(boolean, boolean) - Method in class org.anchoranalysis.image.voxel.object.ObjectCollection
-
A string representation of all objects in the collection using their center of gravities (and optionally indices)
- toStringUnixStyle(String) - Static method in class org.anchoranalysis.core.system.path.FilePathToUnixStyleConverter
-
Converts a path to a string using Unix-style separators (forward-slashes)
- toStringUnixStyle(Path) - Static method in class org.anchoranalysis.core.system.path.FilePathToUnixStyleConverter
-
Converts a path to a string using Unix-style separators (forward-slashes)
- total() - Method in class org.anchoranalysis.feature.results.ResultsVector
- totalAll(MemoCollection, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
- TotalCount - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- TotalCount() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.TotalCount
- totalIndividual(VoxelizedMarkMemo, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.scheme.EnergySchemeWithSharedFeatures
- totalMinusGPUs() - Method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
- totalNumber() - Method in class org.anchoranalysis.core.concurrency.ConcurrencyPlan
- totalNumberSlices() - Method in class org.anchoranalysis.io.bioformats.copyconvert.ImageFileShape
-
The total number of z-slices across all frames, channels
- totalNumberVoxelPositions() - Method in class org.anchoranalysis.spatial.Extent
-
Calculates the total number of pixel positions needed to represent this bounding box as a pixel array This is not the same as volume, both the start and end pixel are included
- ToTextFile - Class in org.anchoranalysis.experiment.bean.log
-
Logs to a text-file created in the output-directory under a particular name.
- ToTextFile() - Constructor for class org.anchoranalysis.experiment.bean.log.ToTextFile
- ToTextFileBase - Class in org.anchoranalysis.experiment.bean.log
- ToTextFileBase() - Constructor for class org.anchoranalysis.experiment.bean.log.ToTextFileBase
- ToTextFileOnlyIfFailure - Class in org.anchoranalysis.experiment.bean.log
-
Logs to a text file like with
ToTextFilebut the log is ONLY written if a failure occurs in the experiment. - ToTextFileOnlyIfFailure() - Constructor for class org.anchoranalysis.experiment.bean.log.ToTextFileOnlyIfFailure
- ToThePowerOfConstant<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.arithmetic
- ToThePowerOfConstant() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.arithmetic.ToThePowerOfConstant
- TouchingVoxels - Class in org.anchoranalysis.plugin.image.feature.bean.object.pair.touching
-
Base class for features that calculate touching with a dilated bounding box intersection
- TouchingVoxels() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.object.pair.touching.TouchingVoxels
- ToUnsignedByte - Class in org.anchoranalysis.image.core.channel.convert
-
Converts from other data types to
UnsignedByteBuffer(unsigned 8-bit) without scaling. - ToUnsignedByte - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
- ToUnsignedByte() - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedByte
- ToUnsignedByte() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.ToUnsignedByte
- ToUnsignedByte(VoxelsConverter<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedByte
- ToUnsignedByteScaleByMinMaxValue - Class in org.anchoranalysis.image.core.channel.convert
-
Converts from other data types to
UnsignedByteBuffer(unsigned 8-bit) scaling from the range of the source data-type. - ToUnsignedByteScaleByMinMaxValue(int, int) - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedByteScaleByMinMaxValue
- ToUnsignedShort - Class in org.anchoranalysis.image.core.channel.convert
- ToUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort
- ToUnsignedShort() - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedShort
- ToUnsignedShort(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toshort.ToUnsignedShort
- ToUnsignedShort(VoxelsConverter<UnsignedShortBuffer>) - Constructor for class org.anchoranalysis.image.core.channel.convert.ToUnsignedShort
- toVoxel(int, int, int) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
-
Assigns one particular voxel
- toVoxel(Point3i) - Method in interface org.anchoranalysis.image.voxel.assigner.VoxelsAssigner
-
Assigns one particular voxel
- toVoxels(ImagePlus) - Static method in class org.anchoranalysis.io.imagej.convert.ConvertFromImagePlus
-
Converts an
ImagePlusto aVoxelsWrapper. - transferFrom(int, VoxelBuffer<T>, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
- transferFromConvert(int, VoxelBuffer<?>, int) - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
- transferSlice(int, VoxelsWrapper, int, boolean) - Method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- transferSlicesResizeXY(VoxelsWrapper, VoxelsWrapper, Interpolator) - Static method in class org.anchoranalysis.image.voxel.interpolator.InterpolateUtilities
- transferValue(int, int) - Method in class org.anchoranalysis.math.histogram.Histogram
- transform(Collection<File>) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.LimitWithDirectory
- transform(Collection<File>) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SampleWithDirectory
- transform(Collection<File>) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SortAlphabeticallyWithDirectory
- transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.input.files.provider.FilterForExistingFiles
- transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.Limit
- transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.RandomOrder
- transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.RemoveMatching
- transform(Collection<File>, boolean) - Method in class org.anchoranalysis.plugin.io.bean.provider.file.SortAlphabetically
- transform(Optional<W>, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformMapOptional
- transform(Assignment) - Method in class org.anchoranalysis.annotation.io.assignment.generator.AssignmentGenerator
- transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.ColorSchemeUnary
-
Transform an existing
ColorList. - transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.Prepend
- transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.Repeat
- transform(ColorList) - Method in class org.anchoranalysis.bean.shared.color.scheme.Shuffle
- transform(VoxelizedMarksWithEnergy, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.AddDualTransformer
- transform(ColoredMarksWithDisplayStack) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksGeneratorBase
- transform(MarkCollection) - Method in class org.anchoranalysis.mpp.io.marks.generator.MarksAsUniqueValueGenerator
- transform(MarkCollection, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.PointsFitter
- transform(MarkCollection, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.AddEnergy
- transform(StateTransformer<T, S>, TransformationContext) - Method in class org.anchoranalysis.mpp.segment.optimization.DualState
- transform(DualVoxelizedMarks, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.RetrieveDestinationFromDual
- transform(DualVoxelizedMarks, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.dual.RetrieveSourceFromDual
- transform(MarksFromPartition, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartition
- transform(MarksFromPartition, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.partition.RemovePartitionAndThen
- transform(ToPixelized<T>, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.RetrieveDestinationFromVoxelized
- transform(ToPixelized<T>, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.RetrieveSourceFromVoxelized
- transform(S, TransformationContext) - Method in class org.anchoranalysis.mpp.segment.transformer.Compose
- transform(T) - Method in class org.anchoranalysis.io.generator.OneStageGenerator
- transform(T) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
- transform(T) - Method in interface org.anchoranalysis.io.generator.TransformingGenerator
-
Applies any necessary preprocessing to create an element suitable for writing to the filesystem.
- transform(T) - Method in class org.anchoranalysis.io.generator.TransformingGeneratorBridge
- transform(T, TransformationContext) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
- transform(W, TransformationContext) - Method in interface org.anchoranalysis.mpp.segment.transformer.StateTransformer
- TransformationAssignMode<S,T,U> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
-
Applies a transformation to the kernel-type U to calculate the Energy used as the primary readout during optimization
- TransformationAssignMode() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformationAssignMode
- TransformationContext - Class in org.anchoranalysis.mpp.segment.transformer
- TransformationContext(Dimensions, KernelCalculationContext, Logger) - Constructor for class org.anchoranalysis.mpp.segment.transformer.TransformationContext
- TransformingGenerator<T,S> - Interface in org.anchoranalysis.io.generator
-
Performs preprocessing to transform the element into another type before being written to the filesystem.
- TransformingGeneratorBridge<S,T,V> - Class in org.anchoranalysis.io.generator
-
Allows us to call an
SingleFileTypeGenerator<V,S>as if it was anSingleFileTypeGenerator<T,S>using an function to connect the two. - TransformingGeneratorBridge(TransformingGenerator<V, S>, CheckedFunction<T, V, ? extends Throwable>) - Constructor for class org.anchoranalysis.io.generator.TransformingGeneratorBridge
- TransformMapOptional<W,X> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode
- TransformMapOptional(StateTransformer<W, X>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.mode.TransformMapOptional
- transpose() - Method in class org.anchoranalysis.spatial.rotation.RotationMatrix
- TraversalResult(List<Path>, List<Path>, int) - Constructor for class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter.TraversalResult
- traverse(Point3i, List<Point3i>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.OutlinePixelsRetriever
- traverse(Point3i, List<Point3i>, RandomNumberGenerator) - Method in class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
- TraverseDirectoryForProgressReporter - Class in org.anchoranalysis.core.progress
- TraverseDirectoryForProgressReporter.TraversalResult - Class in org.anchoranalysis.core.progress
- traverseNotRecursive(Path, Predicate<Path>) - Static method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter
- TraverseOutlineException - Exception in org.anchoranalysis.plugin.mpp.bean.outline
- TraverseOutlineException(String) - Constructor for exception org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineException
- TraverseOutlineException(String, Throwable) - Constructor for exception org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineException
- TraverseOutlineOnImage - Class in org.anchoranalysis.plugin.mpp.bean.outline
- TraverseOutlineOnImage() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.TraverseOutlineOnImage
- TraversePointsOnContour - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation
- TraversePointsOnContour() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.fromorientation.TraversePointsOnContour
- traverseRecursive(Path, int, Predicate<Path>, int) - Static method in class org.anchoranalysis.core.progress.TraverseDirectoryForProgressReporter
- trigger() - Method in class org.anchoranalysis.mpp.segment.bean.optimization.termination.TriggerTerminationCondition
- TriggerTerminationCondition - Class in org.anchoranalysis.mpp.segment.bean.optimization.termination
- TriggerTerminationCondition() - Constructor for class org.anchoranalysis.mpp.segment.bean.optimization.termination.TriggerTerminationCondition
- Tuple3d - Class in org.anchoranalysis.spatial.point
- Tuple3d() - Constructor for class org.anchoranalysis.spatial.point.Tuple3d
- Tuple3f - Class in org.anchoranalysis.spatial.point
- Tuple3f() - Constructor for class org.anchoranalysis.spatial.point.Tuple3f
- Tuple3i - Class in org.anchoranalysis.spatial.point
- Tuple3i() - Constructor for class org.anchoranalysis.spatial.point.Tuple3i
- twoNonOverlappingCircles(boolean) - Static method in class org.anchoranalysis.test.feature.plugins.objects.FeatureInputOverlappingCircleFixture
-
Two object-masks of circles in different locations WITHOUT any overlap
- twoOverlappingCircles(boolean) - Static method in class org.anchoranalysis.test.feature.plugins.objects.FeatureInputOverlappingCircleFixture
-
Two object-masks of circles in different locations WITH some overlap
- TwoVoxelMappingBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
Takes the two channels and creates a NEW third channel whose pixels are a function of the two channels
- TwoVoxelMappingBase(IntBinaryOperation) - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.TwoVoxelMappingBase
- TypedEdge<V,P> - Class in org.anchoranalysis.core.graph
-
An edge that exists in a graph, together with the two vertices that it conntects.
- TypedEdge(P, V, V) - Constructor for class org.anchoranalysis.core.graph.TypedEdge
- TypedValue - Class in org.anchoranalysis.core.value
- TypedValue(double, int) - Constructor for class org.anchoranalysis.core.value.TypedValue
- TypedValue(int) - Constructor for class org.anchoranalysis.core.value.TypedValue
- TypedValue(String) - Constructor for class org.anchoranalysis.core.value.TypedValue
- TypedValue(String, boolean) - Constructor for class org.anchoranalysis.core.value.TypedValue
U
- UnaryWithChannelBase - Class in org.anchoranalysis.plugin.image.bean.object.provider
- UnaryWithChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.UnaryWithChannelBase
- UnaryWithMaskBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask
- UnaryWithMaskBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.UnaryWithMaskBase
- UnaryWithObjectsBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider
- UnaryWithObjectsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithObjectsBase
- UnaryWithValueBase - Class in org.anchoranalysis.plugin.image.bean.channel.provider
-
A
ChannelProviderUnarywhich has a scalar value field - UnaryWithValueBase() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.UnaryWithValueBase
- UnchangingEnergy - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
-
TODO consider renaming to ConstantScore
- UnchangingEnergy() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingEnergy
- UnchangingNumberMarks - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination
-
TODO consider renaming to constant size
- UnchangingNumberMarks() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.termination.UnchangingNumberMarks
- unconvertedDataType() - Method in class org.anchoranalysis.image.core.stack.DisplayStack
- underlyingBytes() - Method in class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
-
An array of bytes that underlies the buffer (and can be written into a file).
- UniformProposal<S> - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme
-
Repeatedly propose new collections of marks and take the collection with optimal energy.
- UniformProposal() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.scheme.UniformProposal
- UniformRandom - Class in org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection
- UniformRandom - Class in org.anchoranalysis.plugin.mpp.bean.proposer.position
- UniformRandom() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.mark.single.fromcollection.UniformRandom
- UniformRandom() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.position.UniformRandom
- UniformRandomRadiiProposer - Class in org.anchoranalysis.plugin.mpp.bean.proposer.radii
- UniformRandomRadiiProposer() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
- UniformRandomRadiiProposer(Bound, boolean) - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.radii.UniformRandomRadiiProposer
- union() - Method in class org.anchoranalysis.spatial.box.BoundingBox
-
For performing a union between this bounding-box and another
- uniqueIdentifierFor(FeatureInputPairObjects) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.PairNeighbors
- uniqueIdentifierFor(FeatureInputSingleObject) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.EachObjectIndependently
- uniqueIdentifierFor(T) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.combine.CombineObjectsForFeatures
-
Generates a unique identifier for a particular input
- uniqueIdentifierFor(T) - Method in class org.anchoranalysis.plugin.image.task.feature.calculator.CalculateFeaturesForObjects
- uniquelyIdentifyAllProperties() - Method in class org.anchoranalysis.plugin.image.feature.bean.morphological.MorphologicalIterations
-
A string that uniquely identifies all properties in the bean, but NOT friendly to humans
- uniqueName() - Method in interface org.anchoranalysis.bean.GenerateUniqueParameterization
-
A string describing this class and all its parameterization that is guaranteed to be unique for a given set of parameters
- uniqueName() - Method in class org.anchoranalysis.bean.shared.relation.RelationBean
- uniqueName() - Method in class org.anchoranalysis.bean.shared.relation.threshold.RelationToConstant
- uniqueName() - Method in class org.anchoranalysis.image.bean.threshold.relation.BinaryVoxelsBase
- uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.CenterSliceWindow
- uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.GreatestAreaSlice
- uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.IndexedRegionBase
- uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesBase
- uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.SelectSlicesWithIndexBase
- uniqueName() - Method in class org.anchoranalysis.plugin.mpp.bean.region.Thresholded
- unitArea() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- unitConvert() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
-
Converts voxelized measurements to/from physical units.
- unitConvert() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
-
Converts voxelized measurements to/from physical units.
- UnitConverter - Class in org.anchoranalysis.image.core.dimensions
-
Converts from voxelized units to different physical measurements of area / volume / distance.
- UnitConverter - Class in org.anchoranalysis.plugin.mpp.feature.bean.unit
-
Converts units (distance, area, volume) to a another representation (e.g.
- UnitConverter() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.unit.UnitConverter
- UnitConverter(Resolution) - Constructor for class org.anchoranalysis.image.core.dimensions.UnitConverter
- unitConvertOptional() - Method in class org.anchoranalysis.plugin.image.bean.object.provider.merge.MergeBase
- UnitsWithinRange<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.plugin.image.feature.bean.physical
-
Checks if a value lies within a range defined by units (a minimum and maximum boundary)
- UnitsWithinRange() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.physical.UnitsWithinRange
- UnitTestCompareUtilities - Class in org.anchoranalysis.test.experiment.launcher
- UnitValueArea - Class in org.anchoranalysis.image.bean.unitvalue.extent.area
- UnitValueArea() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
- UnitValueArea(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.area.UnitValueArea
- UnitValueAreaOrVolume - Class in org.anchoranalysis.image.bean.unitvalue.extent
- UnitValueAreaOrVolume() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.UnitValueAreaOrVolume
- UnitValueDistance - Class in org.anchoranalysis.image.bean.unitvalue.distance
- UnitValueDistance() - Constructor for class org.anchoranalysis.image.bean.unitvalue.distance.UnitValueDistance
- UnitValueException - Exception in org.anchoranalysis.image.bean.nonbean.error
- UnitValueException(Exception) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.UnitValueException
- UnitValueException(String) - Constructor for exception org.anchoranalysis.image.bean.nonbean.error.UnitValueException
- UnitValueVolume - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume
- UnitValueVolume() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.UnitValueVolume
- unitVolume() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- UnsignedBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive
-
Base class for buffers that represent an unsigned-type in the signed-equivalent-type NIO
Buffer. - UnsignedBuffer(Buffer) - Constructor for class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBuffer
- UnsignedBufferAsInt - Class in org.anchoranalysis.image.voxel.buffer.primitive
-
A
UnsignedBufferthat exposes its internal types asint. - UnsignedBufferAsInt(Buffer) - Constructor for class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedBufferAsInt
- unsignedByteArray(byte[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
-
Wraps an existing array (encoding unsigned bytes as a signed array) as a voxel-buffer.
- unsignedByteBuffer(UnsignedByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
-
Wraps an unsigned-byte buffer into a voxel-buffer.
- UnsignedByteBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive
-
Wraps a
ByteBufferbut automatically performs conversion toint. - UnsignedByteFromFloat - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
- UnsignedByteFromFloat(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromFloat
- UnsignedByteFromUnsignedByteInterleaving - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
- UnsignedByteFromUnsignedByteInterleaving() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteInterleaving
- UnsignedByteFromUnsignedByteNoInterleaving - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
- UnsignedByteFromUnsignedByteNoInterleaving() - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedByteNoInterleaving
- UnsignedByteFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
- UnsignedByteFromUnsignedInt(int, boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedInt
- UnsignedByteFromUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.tobyte
- UnsignedByteFromUnsignedShort(boolean, int) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.tobyte.UnsignedByteFromUnsignedShort
- unsignedByteRaw(ByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
-
Wraps an unsigned-byte buffer (represented by a NIO signed-buffer) into a voxel-buffer.
- unsignedByteToInt(byte) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
- unsignedByteToShort(byte) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
- UnsignedByteVoxelType - Class in org.anchoranalysis.image.voxel.datatype
- unsignedIntArray(int[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
-
Wraps an unsigned-int buffer into a voxel-buffer.
- unsignedIntBuffer(UnsignedIntBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
-
Wraps an unsigned-int buffer (represented by a NIO signed-buffer) into a voxel-buffer.
- UnsignedIntBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive
-
Wraps an
IntBufferbut automatically performs conversion tolong. - UnsignedIntFromUnsignedInt - Class in org.anchoranalysis.io.bioformats.copyconvert.toint
- UnsignedIntFromUnsignedInt(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toint.UnsignedIntFromUnsignedInt
- unsignedIntToInt(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
- unsignedIntToLong(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
- unsignedIntToShort(int) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
- UnsignedIntVoxelType - Class in org.anchoranalysis.image.voxel.datatype
- unsignedShortArray(short[]) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
-
Wraps an existing array (encoding unsigned shorts as a signed array) as a voxel-buffer.
- unsignedShortBuffer(UnsignedShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
-
Wraps an unsigned-short buffer into a voxel-buffer.
- UnsignedShortBuffer - Class in org.anchoranalysis.image.voxel.buffer.primitive
-
Wraps a
ShortBufferbut automatically performs conversion toint. - UnsignedShortFromSignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort
- UnsignedShortFromSignedShort(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromSignedShort
- UnsignedShortFromUnsignedShort - Class in org.anchoranalysis.io.bioformats.copyconvert.toshort
- UnsignedShortFromUnsignedShort(boolean) - Constructor for class org.anchoranalysis.io.bioformats.copyconvert.toshort.UnsignedShortFromUnsignedShort
- unsignedShortRaw(ShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.VoxelBufferWrap
-
Wraps an unsigned-short buffer (represented by a NIO signed-buffer) into a voxel-buffer.
- unsignedShortToInt(short) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.PrimitiveConverter
- UnsignedShortVoxelType - Class in org.anchoranalysis.image.voxel.datatype
- UnsignedVoxelType - Class in org.anchoranalysis.image.voxel.datatype
- UnsignedVoxelType(int, String, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.UnsignedVoxelType
- UnsupportedMarkTypeException - Exception in org.anchoranalysis.mpp.mark
- UnsupportedMarkTypeException(Exception) - Constructor for exception org.anchoranalysis.mpp.mark.UnsupportedMarkTypeException
- UnsupportedMarkTypeException(String) - Constructor for exception org.anchoranalysis.mpp.mark.UnsupportedMarkTypeException
- untilFirstIntensityEqualTo(BoundedVoxels<UnsignedByteBuffer>, byte) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsEqualTo
-
Iterates each voxel until a specific intensity value is found.
- UpdatableBeforeCondition - Interface in org.anchoranalysis.plugin.image.object.merge.condition
-
Rather than checking if obj1 vs obj2 is accepted instead there's a two stage process
- UpdatableMarkSet - Interface in org.anchoranalysis.mpp.mark.set
- UpdatablePointsContainer - Class in org.anchoranalysis.mpp.bean.points.updatable
- UpdatablePointsContainer() - Constructor for class org.anchoranalysis.mpp.bean.points.updatable.UpdatablePointsContainer
- update() - Method in class org.anchoranalysis.core.progress.ProgressReporterIncrement
- update(double) - Method in class org.anchoranalysis.core.progress.ProgressReporterMultiple
- update(int) - Method in interface org.anchoranalysis.core.progress.ProgressReporter
- update(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterConsole
- update(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterNull
- update(int) - Method in class org.anchoranalysis.core.progress.ProgressReporterOneOfMany
- update(Integer) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncreasingIntegers
- update(Integer) - Method in class org.anchoranalysis.io.manifest.sequencetype.IncrementingIntegers
- update(String) - Method in class org.anchoranalysis.io.manifest.sequencetype.StringsWithoutOrder
- update(Point2d, Point2d, Orientation2D) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
- update(T) - Method in class org.anchoranalysis.io.manifest.sequencetype.SequenceType
- updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelBirthAndKill
- updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelExchange
- updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksVoxelized
- updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelMerge
- updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelSplit
- updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelBirthPixelized
- updateAfterAcceptance(ListUpdatableMarkSetCollection, VoxelizedMarksWithEnergy, VoxelizedMarksWithEnergy) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.pixelized.KernelDeathPixelized
- updateAfterAcceptance(ListUpdatableMarkSetCollection, MarkCollection, MarkCollection) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksProposed
- updateAfterAcceptance(ListUpdatableMarkSetCollection, MarksFromPartition, MarksFromPartition) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelBirthPartition
- updateAfterAcceptance(ListUpdatableMarkSetCollection, MarksFromPartition, MarksFromPartition) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.dependent.mark.KernelDeathPartition
- updateAfterAcceptance(ListUpdatableMarkSetCollection, MarksFromPartition, MarksFromPartition) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelInitialMarksFromPartition
- updateAfterAcceptance(ListUpdatableMarkSetCollection, T, T) - Method in class org.anchoranalysis.mpp.segment.bean.kernel.Kernel
-
If the kernel is accepted, makes the necessary changes to a ListUpdatableMarkSetCollection
- updateAfterAcceptance(ListUpdatableMarkSetCollection, T, T) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.kernel.independent.KernelReplace
- updateAfterMarkChange() - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.PointList
- updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.PointListBase
- updateAfterPointsChange() - Method in class org.anchoranalysis.mpp.mark.points.Polygon
- updateIndex(String, int) - Method in class org.anchoranalysis.io.generator.sequence.SequenceMemory
- updateLabeling(double) - Method in class org.anchoranalysis.math.optimization.HungarianAlgorithm
-
Update labels with the specified slack by adding the slack value for committed workers and by subtracting the slack value for committed jobs.
- UpdateMarkSetException - Exception in org.anchoranalysis.mpp.mark.set
- UpdateMarkSetException(Exception) - Constructor for exception org.anchoranalysis.mpp.mark.set.UpdateMarkSetException
- UpdateMarkSetException(String) - Constructor for exception org.anchoranalysis.mpp.mark.set.UpdateMarkSetException
- updateResolution(Optional<Resolution>) - Method in class org.anchoranalysis.image.core.channel.Channel
- updateResolution(Resolution) - Method in class org.anchoranalysis.image.core.stack.Stack
- updateShellRad(double) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- updateSlice(int, VoxelBuffer<T>) - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
- updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.AndCondition
- updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.NeighborhoodCondition
- updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in interface org.anchoranalysis.plugin.image.object.merge.condition.UpdatableBeforeCondition
- updateSourceObject(ObjectMask, Optional<UnitConverter>) - Method in class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
- updateTotal(MemoCollection, EnergyStackWithoutParams) - Method in class org.anchoranalysis.mpp.feature.energy.marks.MarksWithEnergyBreakdown
- UpperLowerQuantileIntensity - Class in org.anchoranalysis.image.core.channel.convert.attached.channel
- UpperLowerQuantileIntensity(double, double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.channel.UpperLowerQuantileIntensity
- UpperLowerQuantileIntensityFromHistogram - Class in org.anchoranalysis.image.core.channel.convert.attached.histogram
-
Scales by a lower and upper quantile of the intensity values of an image
- UpperLowerQuantileIntensityFromHistogram(double, double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
- UpperLowerQuantileIntensityFromHistogram(double, double, double, double) - Constructor for class org.anchoranalysis.image.core.channel.convert.attached.histogram.UpperLowerQuantileIntensityFromHistogram
- useDefault() - Static method in class org.anchoranalysis.launcher.executor.selectparam.SelectParamFactory
-
Use default manager.
- UseDefaultManager - Class in org.anchoranalysis.launcher.executor.selectparam
-
Uses whatever default-manager exists
- UseDefaultManager() - Constructor for class org.anchoranalysis.launcher.executor.selectparam.UseDefaultManager
- useDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.Experiment
-
Whether to detail more (a lengthy experiment) or less (something quick and simple - suitable for console)?
- useDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.io.InputOutputExperiment
- useDetailedLogging() - Method in class org.anchoranalysis.experiment.bean.io.OutputExperiment
- useDetailedLogging() - Method in class org.anchoranalysis.plugin.io.bean.experiment.CopyFilesExperiment
- useDetailedLogging() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickExperiment
- useDetailedLogging() - Method in class org.anchoranalysis.plugin.quick.bean.experiment.QuickMultiDatasetExperiment
- useDetailedLogging() - Method in class org.anchoranalysis.plugin.quick.bean.structure.QuickMultiDatasetStructuredExperiment
- useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.CalculateLevelRelativeToThreshold
-
Uses
calculateLevelElseinstead of the standard calculation-level approach - useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfGreaterThan
- useElseInstead(int, int) - Method in class org.anchoranalysis.plugin.image.bean.histogram.threshold.IfLessThan
- useZ - Variable in class org.anchoranalysis.image.voxel.kernel.dilateerode.BinaryKernelMorph3Extent
V
- valueByDimension(int) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- valueByDimension(int) - Method in class org.anchoranalysis.spatial.Extent
- valueByDimension(int) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- valueByDimension(int) - Method in class org.anchoranalysis.spatial.point.Tuple3f
- valueByDimension(AxisType) - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- valueByDimension(AxisType) - Method in class org.anchoranalysis.spatial.Extent
- valueByDimension(AxisType) - Method in class org.anchoranalysis.spatial.point.Tuple3d
- valueByDimension(AxisType) - Method in class org.anchoranalysis.spatial.point.Tuple3f
- valueFor(SessionInput<FeatureInputSingleObject>, ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjects
- valueFor(SessionInput<FeatureInputSingleObject>, ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.FeatureIntersectingObjectsSingleElement
- valueFor(SessionInput<FeatureInputSingleObject>, ResolvedCalculation<ObjectCollection, FeatureInputSingleObject>) - Method in class org.anchoranalysis.plugin.image.feature.bean.object.single.shared.intersecting.NumberIntersectingObjects
- valueFor(AxisType, int, int, int) - Static method in class org.anchoranalysis.spatial.axis.AxisTypeConverter
-
Multiplexes the correct value for the given dimension
- valueFromFirst(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
- valueFromMerged(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
- valueFromSecond(SessionInput<FeatureInputPairObjects>) - Method in class org.anchoranalysis.image.feature.bean.object.pair.FeatureDeriveFromPair
- valueOf(String) - Static method in enum org.anchoranalysis.core.index.bounded.BoundChangeEvent.BoundType
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.anchoranalysis.image.core.channel.convert.ConversionPolicy
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.anchoranalysis.image.voxel.object.morphological.SelectDimensions
-
Returns the enum constant of this type with the specified name.
- valueOf(String) - Static method in enum org.anchoranalysis.spatial.axis.AxisType
-
Returns the enum constant of this type with the specified name.
- values() - Static method in enum org.anchoranalysis.core.index.bounded.BoundChangeEvent.BoundType
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.anchoranalysis.image.core.channel.convert.ConversionPolicy
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.anchoranalysis.image.core.dimensions.SpatialUnits.UnitSuffix
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.anchoranalysis.image.feature.object.calculation.CalculateInputFromPair.Extract
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.anchoranalysis.image.voxel.object.morphological.SelectDimensions
-
Returns an array containing the constants of this enum type, in the order they are declared.
- values() - Static method in enum org.anchoranalysis.spatial.axis.AxisType
-
Returns an array containing the constants of this enum type, in the order they are declared.
- variance() - Method in interface org.anchoranalysis.image.voxel.statistics.VoxelStatistics
- variance() - Method in class org.anchoranalysis.math.histogram.Histogram
- variance() - Method in class org.anchoranalysis.math.statistics.VarianceCalculator
-
Calculate the variance
- Variance - Class in org.anchoranalysis.plugin.image.feature.bean.histogram.statistic
- Variance() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.histogram.statistic.Variance
- VarianceCalculator - Class in org.anchoranalysis.math.statistics
-
Helper class for calculating variance from running variables
- VarianceCalculator() - Constructor for class org.anchoranalysis.math.statistics.VarianceCalculator
- VarianceCalculator(long, long, long) - Constructor for class org.anchoranalysis.math.statistics.VarianceCalculator
- VarianceFilter2D - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments
- VarianceFilter2D() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.filter.moments.VarianceFilter2D
- Vector3d - Class in org.anchoranalysis.spatial.point
- Vector3d() - Constructor for class org.anchoranalysis.spatial.point.Vector3d
- Vector3d(double, double, double) - Constructor for class org.anchoranalysis.spatial.point.Vector3d
- Vector3d(Tuple3d) - Constructor for class org.anchoranalysis.spatial.point.Vector3d
- VectorInDirection - Class in org.anchoranalysis.image.bean.spatial.direction
- VectorInDirection() - Constructor for class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
- VectorInDirection(double, double, double) - Constructor for class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
- VectorInDirection(DirectionVector) - Constructor for class org.anchoranalysis.image.bean.spatial.direction.VectorInDirection
- verifySeedsAreInside(Extent) - Method in class org.anchoranalysis.image.core.object.seed.SeedCollection
- vertices() - Method in class org.anchoranalysis.core.graph.GraphWithPayload
-
The set of all vertices in the graph.
- verticesAsObjects() - Method in class org.anchoranalysis.plugin.image.object.merge.MergeGraph
- VeryBright - Class in org.anchoranalysis.bean.shared.color.scheme
-
Creates a list by repeating a defined list of very bright colors.
- VeryBright() - Constructor for class org.anchoranalysis.bean.shared.color.scheme.VeryBright
- VisitedVoxels - Class in org.anchoranalysis.image.core.outline.traverser.visited
-
All pixels that have been visited so far
- VisitedVoxels() - Constructor for class org.anchoranalysis.image.core.outline.traverser.visited.VisitedVoxels
- VisitScheduler - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
- VisitScheduler() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitScheduler
- VisitSchedulerAnd - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
- VisitSchedulerAnd() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerAnd
- VisitSchedulerConvexAboutRoot - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
- VisitSchedulerConvexAboutRoot() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerConvexAboutRoot
- VisitSchedulerMaxDistanceAlongContour - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
- VisitSchedulerMaxDistanceAlongContour() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerMaxDistanceAlongContour
- VisitSchedulerUniformSample - Class in org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler
- VisitSchedulerUniformSample() - Constructor for class org.anchoranalysis.plugin.mpp.bean.outline.visitscheduler.VisitSchedulerUniformSample
- visualization() - Method in interface org.anchoranalysis.mpp.probmap.ProbMap
- visualization() - Method in class org.anchoranalysis.mpp.probmap.ProbMapObjects
- VisualizeOnBackground - Class in org.anchoranalysis.plugin.mpp.bean.define
-
Adds a visualization for all binary-masks and object-collections that are added using a particular background
- VisualizeOnBackground() - Constructor for class org.anchoranalysis.plugin.mpp.bean.define.VisualizeOnBackground
- volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Circle
- volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipse
- volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Ellipsoid
- volume(int) - Method in class org.anchoranalysis.mpp.mark.conic.Sphere
- volume(int) - Method in class org.anchoranalysis.mpp.mark.Mark
- volume(int) - Method in class org.anchoranalysis.mpp.mark.points.LineSegment
- volume(int) - Method in class org.anchoranalysis.mpp.mark.points.PointList
- volume(int) - Method in class org.anchoranalysis.mpp.mark.points.Polygon
- volume(int) - Method in class org.anchoranalysis.mpp.mark.points.PolygonCurve
- volume(int) - Method in class org.anchoranalysis.mpp.mark.points.RotatableBoundingBox
- Volume<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
-
Calculates the volume (x, y and z dimensions) of the scene from the dimensions
- Volume - Class in org.anchoranalysis.plugin.mpp.feature.bean.mark.region
- Volume() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.Volume
- Volume() - Constructor for class org.anchoranalysis.plugin.mpp.feature.bean.mark.region.Volume
- volumeAgg(VoxelizedMarkMemo, VoxelizedMarkMemo, int, RelationBean, LongBinaryOperator) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
- VolumeMin - Class in org.anchoranalysis.plugin.mpp.bean.check
- VolumeMin() - Constructor for class org.anchoranalysis.plugin.mpp.bean.check.VolumeMin
- VolumePhysical - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume
- VolumePhysical() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumePhysical
- volumeStatistic(VoxelizedMarkMemo, VoxelizedMarkMemo, int, RelationBean, LongBinaryOperator) - Method in class org.anchoranalysis.plugin.mpp.feature.bean.memo.pair.overlap.OverlapMaskBase
- VolumeVoxels - Class in org.anchoranalysis.image.bean.unitvalue.extent.volume
- VolumeVoxels() - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
- VolumeVoxels(double) - Constructor for class org.anchoranalysis.image.bean.unitvalue.extent.volume.VolumeVoxels
- volumeXY() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- volumeXY() - Method in class org.anchoranalysis.image.voxel.buffer.mean.MeanIntensityBuffer
-
How many pixels in an XY slice
- volumeXY() - Method in class org.anchoranalysis.spatial.Extent
- voxel(ReadableTuple3i) - Method in class org.anchoranalysis.image.voxel.extracter.Base
- voxel(ReadableTuple3i) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
-
Gets the value of one particular value
- voxelAtBufferIndex(T, int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
- VoxelBuffer<T> - Class in org.anchoranalysis.image.voxel.buffer
-
A buffer of voxel-values, usually corresponding to a single z-slice in
Voxels. - VoxelBuffer() - Constructor for class org.anchoranalysis.image.voxel.buffer.VoxelBuffer
- VoxelBufferFactory - Class in org.anchoranalysis.image.voxel.buffer
-
Creating voxel-buffers and arrays of voxel-buffers of various types.
- VoxelBufferWrap - Class in org.anchoranalysis.image.voxel.buffer
-
Wraps arrays and buffers of primitive-types into
VoxelBuffer. - VoxelDataType - Class in org.anchoranalysis.image.voxel.datatype
-
The type of data one voxel represents in an image-channel.
- VoxelDataType(int, String, long, long) - Constructor for class org.anchoranalysis.image.voxel.datatype.VoxelDataType
- VoxelDataTypeFactoryMultiplexer<T> - Class in org.anchoranalysis.image.voxel.datatype
-
Multiplexes between factories for the various
VoxelDataTypes. - VoxelDataTypeFactoryMultiplexer(T, T, T, T) - Constructor for class org.anchoranalysis.image.voxel.datatype.VoxelDataTypeFactoryMultiplexer
- voxelized() - Method in class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
-
A voxelized-respentation of the mark
- VoxelizedMark - Interface in org.anchoranalysis.mpp.mark.voxelized
-
A voxelized representation of a Mark i.e.
- VoxelizedMarkFactory - Class in org.anchoranalysis.mpp.mark.voxelized
- VoxelizedMarkMemo - Class in org.anchoranalysis.mpp.mark.voxelized.memo
-
Memoization of retrieving a
VoxelizedMarkfrom a mark - VoxelizedMarkMemo(Mark, EnergyStackWithoutParams, RegionMap) - Constructor for class org.anchoranalysis.mpp.mark.voxelized.memo.VoxelizedMarkMemo
- VoxelizedMarksChangeReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- VoxelizedMarksChangeReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksChangeReporter
- VoxelizedMarksPeriodicReporter - Class in org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter
- VoxelizedMarksPeriodicReporter() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.optimization.reporter.VoxelizedMarksPeriodicReporter
- VoxelizedMarksWithEnergy - Class in org.anchoranalysis.mpp.feature.energy.marks
-
A collection of marks, their voxelized equivalents, and associated energy.
- VoxelizedMarksWithEnergy(MarksWithEnergyBreakdown, EnergyStack, SharedFeatureMulti, Logger) - Constructor for class org.anchoranalysis.mpp.feature.energy.marks.VoxelizedMarksWithEnergy
- VoxelizedMarksWithEnergyFactory - Class in org.anchoranalysis.plugin.mpp.segment.optimization
- VoxelizeWithTransform<T> - Class in org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized
-
Converts a Marks to a MarksToPixelized using a transformer
- VoxelizeWithTransform() - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
- VoxelizeWithTransform(StateTransformerBean<T, VoxelizedMarksWithEnergy>) - Constructor for class org.anchoranalysis.plugin.mpp.segment.bean.marks.voxelized.VoxelizeWithTransform
- VoxelPartition<T> - Interface in org.anchoranalysis.mpp.voxel.partition
-
A partition of voxels
- VoxelPartitionFactory<T> - Interface in org.anchoranalysis.mpp.voxel.partition.factory
- VoxelPartitionFactoryHistogramReuse - Class in org.anchoranalysis.mpp.voxel.partition.factory
- VoxelPartitionFactoryHistogramReuse() - Constructor for class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitionFactoryHistogramReuse
- VoxelPartitionHistogram - Class in org.anchoranalysis.mpp.voxel.partition
- VoxelPartitionHistogram(int, Supplier<Histogram>) - Constructor for class org.anchoranalysis.mpp.voxel.partition.VoxelPartitionHistogram
- VoxelPartitonFactoryHistogram - Class in org.anchoranalysis.mpp.voxel.partition.factory
- VoxelPartitonFactoryHistogram() - Constructor for class org.anchoranalysis.mpp.voxel.partition.factory.VoxelPartitonFactoryHistogram
- VoxelPhysicalSize<T extends FeatureInputEnergy> - Class in org.anchoranalysis.plugin.image.feature.bean.dimensions
-
The physical size of a pixel in a specific dimension.
- VoxelPhysicalSize() - Constructor for class org.anchoranalysis.plugin.image.feature.bean.dimensions.VoxelPhysicalSize
- voxels - Variable in class org.anchoranalysis.image.voxel.extracter.Base
-
The voxels to extract from
- voxels() - Method in class org.anchoranalysis.image.core.channel.Channel
- voxels() - Method in class org.anchoranalysis.image.core.mask.Mask
- voxels() - Method in class org.anchoranalysis.image.voxel.binary.BinaryVoxels
-
Voxels that should only have two intensity-values (representing ON and OFF states).
- voxels() - Method in class org.anchoranalysis.image.voxel.BoundedVoxels
-
Voxel-data that fits inside the bounding-box (its extent is invariant with the extent of the bounding-box).
- voxels() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- voxels() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
- voxels() - Method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.EncodedVoxels
- Voxels<T> - Class in org.anchoranalysis.image.voxel
-
A box (3-dimensions) with voxel-data.
- Voxels(SliceBufferIndex<T>, VoxelsFactoryTypeBound<T>, VoxelsArithmetic) - Constructor for class org.anchoranalysis.image.voxel.Voxels
- VoxelsArithmetic - Interface in org.anchoranalysis.image.voxel.arithmetic
- VoxelsArithmeticFactory - Class in org.anchoranalysis.image.voxel.arithmetic
- VoxelsAsFloat - Class in org.anchoranalysis.image.voxel
- VoxelsAsFloat(SliceBufferIndex<FloatBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsAsFloat
- VoxelsAsInt - Class in org.anchoranalysis.image.voxel
- VoxelsAsInt(SliceBufferIndex<UnsignedIntBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsAsInt
- VoxelsAsShort - Class in org.anchoranalysis.image.voxel
- VoxelsAsShort(SliceBufferIndex<UnsignedShortBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsAsShort
- VoxelsAssigner - Interface in org.anchoranalysis.image.voxel.assigner
-
Assigns values to some or all voxels
- VoxelsAssignerFactory - Class in org.anchoranalysis.image.voxel.assigner
- VoxelsConverter<T> - Class in org.anchoranalysis.image.voxel.convert
-
Converts voxels from one data-type to another.
- VoxelsConverter() - Constructor for class org.anchoranalysis.image.voxel.convert.VoxelsConverter
- VoxelScore - Class in org.anchoranalysis.image.feature.bean.score
-
Calculates a per-voxel score
- VoxelScore() - Constructor for class org.anchoranalysis.image.feature.bean.score.VoxelScore
- voxelsEqualTo(int) - Method in class org.anchoranalysis.image.core.channel.Channel
-
Operations on whether particular voxels are equal to a particular value
- voxelsEqualTo(int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
- voxelsEqualTo(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
-
Operations on whether particular voxels are equal to a particular value
- VoxelsExtracter<T> - Interface in org.anchoranalysis.image.voxel.extracter
-
Provides method to read/copy/duplicate portions of voxels
- VoxelsExtracterFactory - Class in org.anchoranalysis.image.voxel.extracter
- VoxelsFactory - Class in org.anchoranalysis.image.voxel.factory
- VoxelsFactoryTypeBound<T> - Interface in org.anchoranalysis.image.voxel.factory
-
A factory for creating voxels with a particular buffer-type
- voxelsGreaterThan(int) - Method in class org.anchoranalysis.image.core.channel.Channel
-
Operations on whether particular voxels are greater than a treshold (but not equal to)
- voxelsGreaterThan(int) - Method in class org.anchoranalysis.image.voxel.extracter.Base
- voxelsGreaterThan(int) - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
-
Operations on whether particular voxels are greater than a treshold (but not equal to)
- voxelsMaximumIntensityProjection() - Method in interface org.anchoranalysis.mpp.mark.voxelized.VoxelizedMark
- voxelsOff() - Method in class org.anchoranalysis.image.core.mask.Mask
- voxelsOff() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- voxelsOn() - Method in class org.anchoranalysis.image.core.mask.Mask
- voxelsOn() - Method in class org.anchoranalysis.image.voxel.object.ObjectMask
- VoxelsPredicate - Interface in org.anchoranalysis.image.voxel.extracter.predicate
-
Methods to find or count voxels that satisfy a predicate.
- VoxelStatistics - Interface in org.anchoranalysis.image.voxel.statistics
-
Allows retrieval of statistics about voxel intensities.
- VoxelStatisticsCombined - Class in org.anchoranalysis.image.voxel.statistics
- VoxelStatisticsCombined() - Constructor for class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsCombined
- VoxelStatisticsFromHistogram - Class in org.anchoranalysis.image.voxel.statistics
- VoxelStatisticsFromHistogram(Histogram) - Constructor for class org.anchoranalysis.image.voxel.statistics.VoxelStatisticsFromHistogram
- VoxelsThresholder - Class in org.anchoranalysis.image.voxel.thresholder
-
Performs threshold operation on voxels.
- VoxelsUnsignedByte - Class in org.anchoranalysis.image.voxel
- VoxelsUnsignedByte(SliceBufferIndex<UnsignedByteBuffer>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsUnsignedByte
- VoxelsWrapper - Class in org.anchoranalysis.image.voxel
-
Wraps a voxels associated with a channel so it can be easily casted to an appropriate data type
- VoxelsWrapper(Voxels<?>) - Constructor for class org.anchoranalysis.image.voxel.VoxelsWrapper
- VoxelsWrapperList - Class in org.anchoranalysis.image.voxel
- VoxelsWrapperList() - Constructor for class org.anchoranalysis.image.voxel.VoxelsWrapperList
- voxelWithMaxIntensity() - Method in interface org.anchoranalysis.image.voxel.extracter.VoxelsExtracter
-
Finds the maximum-value of any voxel and rounds up (ceiling) to nearest long
W
- WatershedEncoding - Class in org.anchoranalysis.plugin.image.segment.watershed.encoding
- WatershedEncoding() - Constructor for class org.anchoranalysis.plugin.image.segment.watershed.encoding.WatershedEncoding
- WatershedYeong - Class in org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong
-
A 'rainfall' watershed algorithm
- WatershedYeong() - Constructor for class org.anchoranalysis.plugin.image.bean.object.segment.channel.watershed.yeong.WatershedYeong
- WeightedKernel<T> - Class in org.anchoranalysis.mpp.segment.kernel.proposer
-
A kernel with an associated weight.
- WeightedKernel(Kernel<T>, double) - Constructor for class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernel
-
Constructor for single kernel factory
- WeightedKernelList<T> - Class in org.anchoranalysis.mpp.segment.kernel.proposer
- WeightedKernelList() - Constructor for class org.anchoranalysis.mpp.segment.kernel.proposer.WeightedKernelList
- weightFor(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ConstantWeight
- weightFor(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.ExtractWeightFromMark
- weightFor(Mark) - Method in class org.anchoranalysis.plugin.mpp.segment.bean.marks.weight.NumberPoints
- weightWidthDescription() - Method in class org.anchoranalysis.annotation.io.bean.AnnotatorStrategy
- weightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.MarkProposerStrategy
- weightWidthDescription() - Method in class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
- WholeImageLabelAnnotationReader - Class in org.anchoranalysis.annotation.io.image
- WholeImageLabelAnnotationReader() - Constructor for class org.anchoranalysis.annotation.io.image.WholeImageLabelAnnotationReader
- WholeImageLabelAnnotationWriter - Class in org.anchoranalysis.annotation.io.image
- WholeImageLabelAnnotationWriter() - Constructor for class org.anchoranalysis.annotation.io.image.WholeImageLabelAnnotationWriter
- WholeImageLabelStrategy - Class in org.anchoranalysis.plugin.annotation.bean.strategy
- WholeImageLabelStrategy() - Constructor for class org.anchoranalysis.plugin.annotation.bean.strategy.WholeImageLabelStrategy
- with(Feature<T>, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
-
Starts a feature-session for a single feature
- with(Feature<T>, FeatureInitParams, SharedFeatureMulti, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
- with(Feature<T>, SharedFeatureMulti, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
-
Starts a feature-session for a single feature
- with(FeatureList<T>, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
-
Starts a feature-session for a list of features
- with(FeatureList<T>, FeatureInitParams, Optional<SharedFeatureMulti>, Logger, BoundReplaceStrategy<T, ? extends ReplaceStrategy<T>>) - Static method in class org.anchoranalysis.feature.session.FeatureSession
- with(FeatureList<T>, FeatureInitParams, SharedFeatureMulti, Logger) - Static method in class org.anchoranalysis.feature.session.FeatureSession
- with(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection
- with(BoundingBox) - Method in class org.anchoranalysis.spatial.box.BoundingBoxUnion
-
Performs a union with another box (immutably)
- withBuffer(Optional<ObjectMask>, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional
-
Iterate over each voxel on an object-mask with one associated buffer.
- withBuffer(Mask, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.core.mask.IterateVoxelsMask
-
Iterate over each voxel in a mask - with an associated buffer for each slice from a voxel-bo
- withBuffer(ObjectMask, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
-
Iterate over each voxel in an object-mask - with one associated buffer for each slice from
Voxels. - withBuffer(Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
-
Iterate over each voxel - with one associated buffer for each slice.
- withBuffer(BoundingBox, Voxels<T>, ProcessBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
-
Iterate over each voxel in a bounding-box - with one associated buffer for each slice
- withCalculateLevel(Histogram, CalculateLevel) - Static method in class org.anchoranalysis.plugin.image.intensity.HistogramThresholder
-
Retains the portion of the histogram greater or equal to the calculated-level
- WithChannelBase - Class in org.anchoranalysis.plugin.image.bean.object.provider
- WithChannelBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithChannelBase
- WithConfidence<T> - Class in org.anchoranalysis.plugin.image.segment
-
Wraps an element with a confidence-score and imposes an ordering (highest confidence first).
- WithConfidence(T, double) - Constructor for class org.anchoranalysis.plugin.image.segment.WithConfidence
- WithContainerBase - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Base class for
ObjectCollectionProviderthat take an optionalobjectsContainerbean-field. - WithContainerBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithContainerBase
- WithDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Base class for
ObjectCollectionProviderUnaryclasses that require dimensions to be specified. - WithDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithDimensionsBase
- within(Optional<ObjectMask>, Extent, ProcessVoxelNeighborAbsolute<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory
-
Within either an object-mask or an extent (as a fallback)
- withinExtent(ProcessVoxelNeighborAbsoluteWithSlidingBuffer<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory
- withinMask(ObjectMask, ProcessChangedPointAbsoluteMasked<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory
- withinMask(ObjectMask, ProcessVoxelNeighborAbsolute<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborFactory
- withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.CompareWithRange
- withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.feature.CompareWithRangeFeature
- withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfConditionWithinRange
- withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.IfOutsideRange
- withinRangeValue(double, SessionInput<T>) - Method in class org.anchoranalysis.plugin.operator.feature.bean.range.RangeCompareBase
-
What value to return if the value is inside the range
- withInside(BoundingBox, Extent) - Method in class org.anchoranalysis.spatial.box.BoundingBoxIntersection
-
Find the intersection and clip to a a containing extent
- withLabel(String) - Method in class org.anchoranalysis.experiment.log.Divider
-
Creates a line of repeated dashes with a centered label of text.
- withMatchingPoints(BoundingBox, Predicate<Point3i>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
-
Iterate over each voxel in a bounding-box that matches a predicate.
- WithOptionalDimensionsBase - Class in org.anchoranalysis.plugin.image.bean.object.provider
-
Base class for
ObjectCollectionProviderUnaryclasses that offer an optional means to specify dimensions. - WithOptionalDimensionsBase() - Constructor for class org.anchoranalysis.plugin.image.bean.object.provider.WithOptionalDimensionsBase
- withoutColor() - Method in class org.anchoranalysis.overlay.collection.ColoredOverlayCollection
- withoutLabel() - Method in class org.anchoranalysis.experiment.log.Divider
-
Creates a line of repeated dashes.
- withoutOrder(OutputPatternStringSuffix) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
-
Writes elements (indexed by strings) to
directory, without any order in the sequence. - withoutOrderCurrentDirectory(String) - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceFactory
-
Writes elements (indexed by strings) to the current directory, without any order in the sequence.
- withoutParams() - Method in class org.anchoranalysis.feature.energy.EnergyStack
-
The energy-stack without associated parameters.
- withoutProgressReporter() - Method in interface org.anchoranalysis.core.progress.CheckedProgressingSupplier
- withoutProperties() - Method in class org.anchoranalysis.image.core.object.properties.ObjectCollectionWithProperties
-
Returns the contained-objects without corresponding properties
- withoutProperties() - Method in class org.anchoranalysis.image.core.object.properties.ObjectWithProperties
- withoutUniformSizeConstraint() - Method in class org.anchoranalysis.image.core.stack.NamedStacksUniformSize
- withPoint(Optional<ObjectMask>, Extent, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional
-
Iterate over all points that are located on a object-mask or else all points in an extent.
- withPoint(ObjectMask, Optional<ObjectMask>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
-
Iterate over each point that is located on an object-mask AND optionally a second-mask
- withPoint(ObjectMask, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
-
Iterate over each voxel that is located on an object-mask
- withPoint(BoundingBox, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
-
Iterate over each voxel in a bounding-box
- withPoint(Extent, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
-
Iterate over each voxel in an
Extent - WithPriority<T> - Class in org.anchoranalysis.core.concurrency
- WithPriority(T, boolean) - Constructor for class org.anchoranalysis.core.concurrency.WithPriority
- WithRadiusBase - Class in org.anchoranalysis.plugin.imagej.bean.channel.provider
-
A
ChannelProviderUnarywith a 'radius' parameter - WithRadiusBase() - Constructor for class org.anchoranalysis.plugin.imagej.bean.channel.provider.WithRadiusBase
- WithResolutionBase<T extends FeatureInputWithResolution> - Class in org.anchoranalysis.image.feature.bean.physical
- WithResolutionBase() - Constructor for class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
- WithResolutionBase(Feature<T>) - Constructor for class org.anchoranalysis.image.feature.bean.physical.WithResolutionBase
- withSlidingBuffer(Optional<ObjectMask>, SlidingBuffer<?>, ProcessPoint) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMaskOptional
-
Iterate over each voxel in a sliding-buffer, optionally restricting it to be only voxels in a certain object
- withThreeBuffers(Voxels<T>, Voxels<T>, Voxels<T>, ProcessBufferTernary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
-
Iterate over each voxel - with three associated buffers for each slice.
- withThreeBuffers(BoundingBox, ReadableTuple3i, ReadableTuple3i, Voxels<T>, Voxels<T>, Voxels<T>, ProcessBufferTernary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
-
Iterate over each voxel in a bounding-box - with three associated buffers for each slice.
- withTwoBuffers(BoundedVoxels<T>, BoundedVoxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded
-
Iterates over the intersection of two bounded-voxels of type
BoundedVoxels. - withTwoBuffers(ObjectMask, Voxels<T>, Voxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
-
Iterate over each voxel with a corresponding ON value in an object-mask - and with two associated buffers for each slice covering the all the global space i.e.
- withTwoBuffers(Voxels<UnsignedByteBuffer>, byte, BoundedVoxels<UnsignedByteBuffer>, BoundedVoxels<UnsignedByteBuffer>, ProcessBufferBinary<UnsignedByteBuffer, UnsignedByteBuffer>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded
-
Iterates over the intersection of two bounded-voxels of type
BoundedVoxelsbut only voxels that lie on an object-mask. - withTwoBuffers(BoundingBox, ReadableTuple3i, Voxels<T>, Voxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
-
Iterate over each voxel in a bounding-box - with two associated buffers for each slice, one
VoxelBufferand oneBuffer - withTwoBuffersAndPoint(Voxels<T>, Voxels<T>, ProcessBufferBinary<T, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
-
Iterate over each voxel - with two associated buffers for each slice
- withTwoBuffersUntil(BoundedVoxels<T>, BoundedVoxels<T>, PredicateBufferBinary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.intersecting.IterateVoxelsIntersectingBounded
-
Iterates over the intersection of two bounded-voxels of type
BoundedVoxelsuntil a predicate is satisfied. - withTwoBuffersUntil(BoundingBox, ReadableTuple3i, Voxels<T>, Voxels<T>, PredicateBufferBinary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
-
Iterate over each voxel in a bounding-box - with two associated buffers for each slice - until a predicate evaluates to true.
- withTwoBuffersWithoutOffset(VoxelBuffer<S>, VoxelBuffer<T>, ProcessBufferBinaryWithoutOffset<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsRemaining
-
Iterate over remaining voxels each voxel - with two associated buffers for each slice.
- withTwoMixedBuffers(BoundingBox, ReadableTuple3i, Voxels<S>, Voxels<T>, ProcessBufferBinaryMixed<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsBoundingBox
-
Iterate over each voxel in a bounding-box - with two associated buffers for each slice.
- withTwoVoxelBuffers(Voxels<S>, Voxels<T>, ProcessVoxelBufferBinary<S, T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
-
Iterate over each voxel in a bounding-box - with two associated voxel-buffers for each slice
- WithValueBase<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean
-
Operations that use a specified constant value
- WithValueBase() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.WithValueBase
- withVoxelBuffer(ObjectMask, Voxels<T>, Optional<BoundingBox>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
-
Iterate over each voxel on an object-mask with one associated
VoxelBuffer. - withVoxelBuffer(ObjectMask, Voxels<T>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsObjectMask
-
Iterate over each voxel on an object-mask with one associated
VoxelBuffer. - withVoxelBuffer(Voxels<T>, ProcessVoxelBufferUnary<T>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
-
Iterate over each voxel - with one associated voxel-buffer for each slice.
- withVoxelBuffer(Voxels<T>, ProcessVoxelBufferUnaryWithPoint<T, E>) - Static method in class org.anchoranalysis.image.voxel.iterator.IterateVoxelsAll
-
Iterate over each voxel - with one associated voxel-buffer for each slice.
- wrap(String, Throwable) - Static method in exception org.anchoranalysis.core.identifier.provider.NamedProviderGetException
- wrap(Voxels<?>) - Static method in class org.anchoranalysis.image.voxel.VoxelsWrapper
- Wrap - Class in org.anchoranalysis.image.voxel.convert.imglib2
- WrapAbsoluteAsMasked<T> - Class in org.anchoranalysis.image.voxel.iterator.neighbor
- WrapAbsoluteAsMasked(ProcessVoxelNeighborAbsolute<T>) - Constructor for class org.anchoranalysis.image.voxel.iterator.neighbor.WrapAbsoluteAsMasked
- WrapAsUpdatable - Class in org.anchoranalysis.plugin.image.object.merge.condition
-
Wraps a BeforeCondition as an UpdatableBefoerCondition
- WrapAsUpdatable(BeforeCondition) - Constructor for class org.anchoranalysis.plugin.image.object.merge.condition.WrapAsUpdatable
- wrapDuplicate(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
-
Wraps an existing list, WITHOUT reusing the list in the internals of the
FeatureListi.e. - wrapRaw(byte[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Exposes a raw byte-array as a buffer with unsigned-bytes.
- wrapRaw(int[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
-
Exposes a raw int-array as a buffer with unsigned-ints.
- wrapRaw(short[]) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
Exposes a raw short-array as a buffer with unsigned-shorts.
- wrapRaw(ByteBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedByteBuffer
-
Exposes a raw
ByteBufferas a buffer with unsigned-bytes. - wrapRaw(IntBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedIntBuffer
-
Exposes a raw
UnsignedIntBufferas a buffer with unsigned-ints. - wrapRaw(ShortBuffer) - Static method in class org.anchoranalysis.image.voxel.buffer.primitive.UnsignedShortBuffer
-
Exposes a raw
UnsignedShortBufferas a buffer with unsigned-shorts. - wrapReuse(List<Feature<T>>) - Static method in class org.anchoranalysis.feature.bean.list.FeatureListFactory
-
Wraps an existing list, reusing the list in the internals of the
FeatureList - WrapStackAsTimeSequence - Class in org.anchoranalysis.image.core.stack.wrap
- WrapStackAsTimeSequence(NamedProvider<Stack>) - Constructor for class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequence
- WrapStackAsTimeSequenceStore - Class in org.anchoranalysis.image.core.stack.wrap
- WrapStackAsTimeSequenceStore(NamedProviderStore<Stack>) - Constructor for class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
- WrapStackAsTimeSequenceStore(NamedProviderStore<Stack>, int) - Constructor for class org.anchoranalysis.image.core.stack.wrap.WrapStackAsTimeSequenceStore
- WrapTimeSequenceAsStack - Class in org.anchoranalysis.image.core.stack.wrap
- WrapTimeSequenceAsStack(NamedProvider<TimeSequence>) - Constructor for class org.anchoranalysis.image.core.stack.wrap.WrapTimeSequenceAsStack
- write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
- write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
- write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in interface org.anchoranalysis.io.output.writer.Writer
-
Writes an element using an
ElementWriterto the current directory. - write(String, ElementWriterSupplier<T>, ElementSupplier<T>) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors
-
Writes an element using an
ElementWriterto the current directory. - write(Collection<T>, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.collection.CollectionGenerator
- write(ImageLabelAnnotation, Path) - Method in class org.anchoranalysis.annotation.io.image.WholeImageLabelAnnotationWriter
- write(DualMarksAnnotation<T>, Path) - Method in class org.anchoranalysis.annotation.io.mark.MarkAnnotationWriter
- write(ObjectCollectionWithProperties, RGBStack, ObjectDrawAttributes) - Method in class org.anchoranalysis.overlay.bean.DrawObject
- write(ObjectCollectionWithProperties, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class org.anchoranalysis.overlay.bean.DrawObject
- write(Manifest, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.combined.ManifestGenerator
- write(S, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.GeneratorBridge
- write(T, Path) - Method in interface org.anchoranalysis.annotation.io.AnnotationWriter
-
Saves the annotation to the filesystem
- write(T, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.combined.CombinedListGenerator
- write(T, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
- write(T, OutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.TransformingGeneratorBridge
- write(T, OutputNameStyle, OutputterChecked) - Method in interface org.anchoranalysis.io.output.writer.ElementWriter
-
Writes a non-indexable output (an output that isn't part of a collection of other similar items)
- writeEnergyStack() - Method in class org.anchoranalysis.mpp.io.output.EnergyStackWriter
- writeFeaturesToCSV(CSVWriter, List<ImageAnnotation>, List<String>) - Method in class org.anchoranalysis.plugin.annotation.bean.aggregate.AnnotationAggregateCSVGenerator
- writeFeaturesToCSV(CSVWriter, ResultsVectorList, List<String>) - Method in class org.anchoranalysis.feature.io.csv.FeatureListCSVGeneratorHorizontal
- writeFeaturesToCSV(CSVWriter, ResultsVectorList, List<String>) - Method in class org.anchoranalysis.feature.io.csv.FeatureListCSVGeneratorVertical
- writeFeaturesToCSV(CSVWriter, T, List<String>) - Method in class org.anchoranalysis.feature.io.csv.FeatureTableCSVGenerator
-
Writes the features to the CSV-file.
- writeFileToOperationRecorder(String, Path, ManifestDescription, String) - Method in class org.anchoranalysis.io.output.outputter.OutputterChecked
-
Writes a file-entry to the operation recorder
- writeGroupedResults(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.feature.SharedStateExportFeatures
-
Writes all the results that have been collected as a CSV file.
- writeGroupOutputInSubdirectory(String, T, ConsistentChannelChecker, InputOutputContext) - Method in class org.anchoranalysis.plugin.image.task.grouped.GroupMapByName
- writeGroupResults(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, InputOutputContext, InputOutputContextSubdirectoryCache) - Method in class org.anchoranalysis.feature.io.results.group.GroupWriter
-
Writes outputs for groups that have been previously added with
GroupWriter.addResultsFor(org.anchoranalysis.feature.io.csv.RowLabels, org.anchoranalysis.feature.results.ResultsVector). - writeHeaders(List<String>) - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
- writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectBase
-
Creates a channel with the levels for a set of objects
- writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectIndependently
- writeLevelsForObjects(Channel, ObjectCollection, Channel) - Method in class org.anchoranalysis.plugin.image.bean.channel.provider.object.LevelPerObjectNeighbors
- writeOffByte(int, UnsignedByteBuffer) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder
- WriteOperationRecorder - Interface in org.anchoranalysis.io.manifest.operationrecorder
-
Makes a record of an output written to the filesystem.
- writeOverlays(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>) - Method in class org.anchoranalysis.overlay.writer.DrawOverlay
-
Writes a collection of colored-overlays to the background
- writeOverlaysIfIntersects(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>, List<BoundingBox>) - Method in class org.anchoranalysis.mpp.io.marks.generator.SimpleOverlayWriter
- writeOverlaysIfIntersects(ColoredOverlayCollection, RGBStack, IdentifierGetter<Overlay>, List<BoundingBox>) - Method in class org.anchoranalysis.overlay.writer.DrawOverlay
- writePrecalculatedMask(RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.overlay.writer.PrecalculationOverlay
- writePrecalculatedOverlays(List<PrecalculationOverlay>, Dimensions, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class org.anchoranalysis.mpp.io.marks.generator.SimpleOverlayWriter
- writePrecalculatedOverlays(List<PrecalculationOverlay>, Dimensions, RGBStack, ObjectDrawAttributes, BoundingBox) - Method in class org.anchoranalysis.overlay.writer.DrawOverlay
- Writer - Interface in org.anchoranalysis.io.output.writer
-
Write data via
ElementWriters to the file system, or creates new sub-directories for writing data to. - writeRaster(FileSaver, String, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter
-
Writes an annotation to the filesystem at
outPath. - writeRaster(FileSaver, String, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.PNG
- writeRaster(FileSaver, String, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.Tiff
- writeResolutionXml(Resolution, Path) - Static method in class org.anchoranalysis.plugin.io.xml.ResolutionAsXml
-
Writes a XML metadata file describing the image-resolution.
- WriteResolutionXml - Class in org.anchoranalysis.plugin.io.bean.stack.writer
-
When writing a stack, an additional file is written to indicate the physical voxel sizes, if this information is known.
- WriteResolutionXml() - Constructor for class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
- writeResultsForAllGroups(Optional<NamedFeatureStore<FeatureInputResults>>, boolean, InputOutputContext) - Method in class org.anchoranalysis.feature.io.results.ResultsWriter
-
Writes the stored-results to CSV files.
- WriterExecuteBeforeEveryOperation - Interface in org.anchoranalysis.io.output.writer
- writeRGBColorToByteArray(RGBColor, Point3i, Dimensions, UnsignedByteBuffer, UnsignedByteBuffer, UnsignedByteBuffer) - Static method in class org.anchoranalysis.image.core.stack.rgb.RGBOutputUtils
- writeRGBMaskToSlice(ObjectMask, BoundingBox, RGBColor, Point3i, int, ReadableTuple3i) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- writeRGBPoint(Point3i, RGBColor) - Method in class org.anchoranalysis.image.core.stack.rgb.RGBStack
- writerMultiplex(boolean) - Method in class org.anchoranalysis.io.output.outputter.Outputter
-
Multiplexes between the
selectiveandpermissivewriters based on a flag. - writeRow(String, int, double) - Method in class org.anchoranalysis.plugin.image.task.slice.SharedStateSelectedSlice
- writeRow(String, String) - Method in class org.anchoranalysis.plugin.image.task.labeller.SharedStateFilteredImageOutput
- writeRow(List<TypedValue>) - Method in class org.anchoranalysis.io.generator.tabular.CSVWriter
- writerPermissive() - Method in class org.anchoranalysis.io.output.outputter.Outputter
-
The writer that allows all outputs.
- WriterRouterErrors - Class in org.anchoranalysis.io.output.writer
-
Write data via
ElementWriters to the file system, or creates new sub-directories for writng data to. - WriterRouterErrors(Writer, ErrorReporter) - Constructor for class org.anchoranalysis.io.output.writer.WriterRouterErrors
- writers() - Method in interface org.anchoranalysis.io.generator.sequence.OutputSequence
- writers() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIncrementing
- writers() - Method in class org.anchoranalysis.io.generator.sequence.OutputSequenceIndexed
- writerSecondLevel(String) - Method in class org.anchoranalysis.io.output.outputter.Outputter
-
A writer that performs a second-level check on which outputs occur, but writes to the top-level directory.
- writerSelective() - Method in class org.anchoranalysis.io.output.outputter.Outputter
-
The writer that allows only certain selected outputs.
- WriterUtilities - Class in org.anchoranalysis.annotation.io
- writeSingle(ObjectWithProperties, RGBStack, ObjectDrawAttributes, int, BoundingBox) - Method in class org.anchoranalysis.overlay.bean.DrawObject
-
Draws a single-object on top of a RGB-stack
- writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter
- writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.BioformatsWriter
- writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.Tiff
- writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
- writeStack(Stack, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
- writeStackAfterCheck(Stack, Path) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.ImageIOWriter
- writeStackAfterCheck(Stack, Path) - Method in class org.anchoranalysis.plugin.opencv.bean.writer.OpenCVWriter
- writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.NoTimeSeries
- writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.SupportsTimeSeries
- writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.bioformats.BioformatsWriter
- writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.RasterWriterDelegateBase
- writeStackSeries(StackSeries, Path, StackWriteOptions) - Method in class org.anchoranalysis.plugin.io.bean.stack.writer.WriteResolutionXml
- writeStackTime(Stack, Path, boolean) - Method in class org.anchoranalysis.io.imagej.bean.stack.writer.ImageJRasterWriter
-
Writes a stack as a time-sequence (many images together in a single file.).
- WriteStringToFile - Class in org.anchoranalysis.io.generator.text
- writeThresholdedByte(int, UnsignedByteBuffer, VoxelBuffer<?>, VoxelBuffer<?>) - Method in class org.anchoranalysis.plugin.image.segment.thresholder.slice.SliceThresholder
- writeToFile(String, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.text.StringGenerator
- writeToFile(Path) - Method in class org.anchoranalysis.core.value.KeyValueParams
-
Serializes the key-value params to a file
- writeToFile(KeyValueParams, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.serialized.KeyValueParamsGenerator
- writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.feature.io.csv.FeatureTableCSVGenerator
- writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.serialized.ObjectOutputStreamGenerator
- writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.serialized.XStreamGenerator
- writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
- writeToFile(T, OutputWriteSettings, Path) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGeneratorBridge
- writeToXML(CSVRow, Element, Document) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.ColumnDefinition
- writeToXML(CSVRow, Element, Document) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Pairwise
- writeToXML(CSVRow, Element, Document) - Method in class org.anchoranalysis.plugin.mpp.experiment.bean.objects.columndefinition.Single
- writeToXML(Element, Document) - Method in class org.anchoranalysis.plugin.mpp.experiment.objects.csv.CSVRow
- writeWithIndex(Collection<T>, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.collection.CollectionGenerator
- writeWithIndex(Manifest, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.combined.ManifestGenerator
- writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.AlwaysAllowed
- writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.CheckIfAllowed
- writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in interface org.anchoranalysis.io.output.writer.Writer
-
Writes an indexed-element using an
ElementWriterin the current directory. - writeWithIndex(IndexableOutputNameStyle, ElementWriterSupplier<T>, ElementSupplier<T>, String) - Method in class org.anchoranalysis.io.output.writer.WriterRouterErrors
-
Writes an indexed-element using an
ElementWriterin the current directory. - writeWithIndex(S, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.GeneratorBridge
- writeWithIndex(T, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.combined.CombinedListGenerator
- writeWithIndex(T, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.SingleFileTypeGenerator
- writeWithIndex(T, String, IndexableOutputNameStyle, OutputterChecked) - Method in class org.anchoranalysis.io.generator.TransformingGeneratorBridge
- writeWithIndex(T, String, IndexableOutputNameStyle, OutputterChecked) - Method in interface org.anchoranalysis.io.output.writer.ElementWriter
-
Writes an indexable output (many outputs of the same type, uniquely identified by an index)
- writeXmlToFile(Document, Path) - Static method in class org.anchoranalysis.io.output.xml.XMLWriter
-
Writes a XML-document to the file-system.
X
- x - Variable in class org.anchoranalysis.spatial.point.Tuple3d
- x - Variable in class org.anchoranalysis.spatial.point.Tuple3f
- x - Variable in class org.anchoranalysis.spatial.point.Tuple3i
- x() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- x() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- x() - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
- x() - Method in class org.anchoranalysis.spatial.Extent
- x() - Method in class org.anchoranalysis.spatial.point.Point2d
- x() - Method in class org.anchoranalysis.spatial.point.Point2f
- x() - Method in class org.anchoranalysis.spatial.point.Point2i
- x() - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
- x() - Method in class org.anchoranalysis.spatial.point.Tuple3d
- x() - Method in class org.anchoranalysis.spatial.point.Tuple3f
- x() - Method in class org.anchoranalysis.spatial.point.Tuple3i
- x() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
- x(float) - Method in class org.anchoranalysis.spatial.point.Tuple3f
- x(int) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains
-
Is this value in the x-dimension within the bounding box range?
- X - org.anchoranalysis.spatial.axis.AxisType
- X_Y_ONLY - org.anchoranalysis.image.voxel.object.morphological.SelectDimensions
-
The dilation applies in X and Y -dimensions only, and not in Z-dimension.
- xFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
- XMLGenerator<T> - Class in org.anchoranalysis.io.generator.xml
- XMLGenerator() - Constructor for class org.anchoranalysis.io.generator.xml.XMLGenerator
- XmlUtilities - Class in org.anchoranalysis.bean.xml
- XMLWriter - Class in org.anchoranalysis.io.output.xml
- Xor - Class in org.anchoranalysis.plugin.image.bean.mask.provider.combine
-
Outputs the logical operation xor (exclusive or) voxelwise on both masks, modifying {mask} with the result.
- Xor() - Constructor for class org.anchoranalysis.plugin.image.bean.mask.provider.combine.Xor
- XStreamDeserializer<T> - Class in org.anchoranalysis.core.serialize
-
Deserializes an object using the XStream library.
- XStreamDeserializer() - Constructor for class org.anchoranalysis.core.serialize.XStreamDeserializer
- XStreamGenerator<T> - Class in org.anchoranalysis.io.generator.serialized
- XStreamGenerator() - Constructor for class org.anchoranalysis.io.generator.serialized.XStreamGenerator
- XStreamGenerator(Optional<String>) - Constructor for class org.anchoranalysis.io.generator.serialized.XStreamGenerator
- XStreamSerializer - Class in org.anchoranalysis.core.serialize
-
Serializes an object using the XStream library.
- XYOrientationExtendToZ - Class in org.anchoranalysis.plugin.mpp.bean.proposer.points
- XYOrientationExtendToZ() - Constructor for class org.anchoranalysis.plugin.mpp.bean.proposer.points.XYOrientationExtendToZ
Y
- y - Variable in class org.anchoranalysis.spatial.point.Tuple3d
- y - Variable in class org.anchoranalysis.spatial.point.Tuple3f
- y - Variable in class org.anchoranalysis.spatial.point.Tuple3i
- y() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- y() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- y() - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
- y() - Method in class org.anchoranalysis.spatial.Extent
- y() - Method in class org.anchoranalysis.spatial.point.Point2d
- y() - Method in class org.anchoranalysis.spatial.point.Point2f
- y() - Method in class org.anchoranalysis.spatial.point.Point2i
- y() - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
- y() - Method in class org.anchoranalysis.spatial.point.Tuple3d
- y() - Method in class org.anchoranalysis.spatial.point.Tuple3f
- y() - Method in class org.anchoranalysis.spatial.point.Tuple3i
- y() - Method in class org.anchoranalysis.spatial.scale.ScaleFactor
- y(float) - Method in class org.anchoranalysis.spatial.point.Tuple3f
- y(int) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains
-
Is this value in the y-dimension within the bounding box range?
- Y - org.anchoranalysis.spatial.axis.AxisType
- yFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
Z
- z - Variable in class org.anchoranalysis.spatial.point.Tuple3d
- z - Variable in class org.anchoranalysis.spatial.point.Tuple3f
- z - Variable in class org.anchoranalysis.spatial.point.Tuple3i
- z() - Method in class org.anchoranalysis.image.core.dimensions.Dimensions
- z() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
- z() - Method in class org.anchoranalysis.image.core.orientation.DirectionVector
- z() - Method in class org.anchoranalysis.spatial.Extent
- z() - Method in interface org.anchoranalysis.spatial.point.ReadableTuple3i
- z() - Method in class org.anchoranalysis.spatial.point.Tuple3d
- z() - Method in class org.anchoranalysis.spatial.point.Tuple3f
- z() - Method in class org.anchoranalysis.spatial.point.Tuple3i
- z(float) - Method in class org.anchoranalysis.spatial.point.Tuple3f
- z(int) - Method in class org.anchoranalysis.spatial.box.BoundingBoxContains
-
Is this value in the z-dimension within the bounding box range?
- Z - org.anchoranalysis.spatial.axis.AxisType
- Z_ONLY - org.anchoranalysis.image.voxel.object.morphological.SelectDimensions
-
The dilation applies only in the Z-dimension.
- zChange - Variable in class org.anchoranalysis.image.voxel.iterator.neighbor.ProcessVoxelNeighborAbsoluteWithSlidingBuffer
- ZeroOutsideMask - Class in org.anchoranalysis.plugin.image.bean.channel.provider.mask
-
Set pixels NOT IN the mask to 0, but keep pixels IN the mask identical.
- ZeroOutsideMask() - Constructor for class org.anchoranalysis.plugin.image.bean.channel.provider.mask.ZeroOutsideMask
- zeroValue(int) - Method in class org.anchoranalysis.math.histogram.Histogram
- zFromChainCode(int) - Static method in class org.anchoranalysis.plugin.image.segment.watershed.encoding.ChainCodesDirection
- zRelative() - Method in class org.anchoranalysis.image.core.dimensions.Resolution
-
Assumes x and y has constant resolution, and gives the relative resolution of z to x or y.
- zScore(double) - Method in class org.anchoranalysis.math.statistics.FirstSecondOrderStatistic
- ZScore<T extends FeatureInput> - Class in org.anchoranalysis.plugin.operator.feature.bean.score
- ZScore() - Constructor for class org.anchoranalysis.plugin.operator.feature.bean.score.ZScore
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